0.009839
0.000000
0.009379
0.000000
0.017581
0.000000
0.000000
0.000000
0.016881
0.00000
0.00000
0.00000
Mas-Droux, C.
Bayliss, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
133.63
90.00
101.640
56.880
81.840
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
Cl -1
35.453
CHLORIDE ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
C29 H29 F3 N4 O3
538.561
4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE
non-polymer
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
CL
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
C
N
90
N
O
N
91
N
C
N
92
N
O
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
N
N
100
S
C
N
101
N
C
N
102
N
O
N
103
N
C
N
104
N
C
N
105
N
C
N
106
N
O
N
107
N
N
N
108
N
O
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
N
N
120
S
C
N
121
N
C
N
122
N
O
N
123
N
C
N
124
N
C
N
125
N
C
N
126
N
O
N
127
N
O
N
128
N
O
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
N
N
139
N
C
N
140
N
C
N
141
N
O
N
142
N
O
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
N
N
149
S
C
N
150
N
C
N
151
N
O
N
152
N
C
Y
153
N
C
Y
154
N
N
Y
155
N
C
Y
156
N
C
Y
157
N
N
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
N
N
173
S
C
N
174
N
C
N
175
N
O
N
176
S
C
N
177
N
C
N
178
N
C
N
179
N
C
N
180
N
O
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
N
N
195
S
C
N
196
N
C
N
197
N
O
N
198
N
C
N
199
N
C
N
200
N
C
N
201
N
C
N
202
N
O
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
C
N
223
N
C
N
224
N
N
N
225
N
O
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
N
N
242
S
C
N
243
N
C
N
244
N
O
N
245
N
C
N
246
N
C
N
247
N
S
N
248
N
C
N
249
N
O
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
N
N
262
S
C
N
263
N
C
N
264
N
O
N
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
N
272
N
O
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
N
N
285
S
C
N
286
N
C
N
287
N
O
N
288
N
C
N
289
N
C
N
290
N
C
N
291
N
O
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
N
N
302
S
C
N
303
N
C
N
304
N
O
N
305
N
C
N
306
N
O
N
307
N
O
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
N
N
316
S
C
N
317
N
C
N
318
N
O
N
319
R
C
N
320
N
O
N
321
N
C
N
322
N
O
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
N
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
N
346
N
O
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
N
370
N
O
N
371
N
O
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
N
388
N
C
N
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
C
N
403
R
C
N
404
N
O
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
N
Y
409
N
C
Y
410
N
N
Y
411
N
C
Y
412
N
C
Y
413
N
C
Y
414
N
C
N
415
N
O
N
416
N
C
N
417
N
C
N
418
N
C
N
419
N
N
N
420
N
C
N
421
N
C
N
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
Y
427
N
C
N
428
N
C
N
429
N
N
N
430
N
O
Y
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
N
437
N
C
N
438
N
F
N
439
N
F
N
440
N
F
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
Y
149
N
sing
Y
150
N
doub
Y
151
N
doub
N
152
N
sing
Y
153
N
sing
N
154
N
sing
Y
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
doub
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
Y
257
N
doub
Y
258
N
sing
Y
259
N
sing
N
260
N
sing
Y
261
N
doub
N
262
N
sing
Y
263
N
doub
N
264
N
sing
Y
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
doub
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
Y
326
N
doub
Y
327
N
sing
Y
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
doub
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
Y
354
N
doub
Y
355
N
sing
Y
356
N
sing
N
357
N
sing
Y
358
N
doub
N
359
N
sing
Y
360
N
doub
N
361
N
sing
Y
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
Y
389
N
sing
Y
390
N
doub
Y
391
N
doub
Y
392
N
sing
Y
393
N
sing
Y
394
N
sing
Y
395
N
sing
Y
396
N
doub
Y
397
N
sing
Y
398
N
sing
Y
399
N
doub
Y
400
N
doub
N
401
N
sing
Y
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
Y
411
N
doub
Y
412
N
sing
Y
413
N
doub
Y
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
doub
Y
418
N
doub
Y
419
N
sing
Y
420
N
sing
Y
421
N
doub
Y
422
N
sing
Y
423
N
doub
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
54
1626
10.1021/JM1011726
21366329
Benzimidazole Inhibitors Induce a Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure-Activity Relationship.
2011
10.2210/pdb2xnp/pdb
pdb_00002xnp
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2010-04-26
ADSC CCD
SINGLE WAVELENGTH
M
x-ray
1
0.97630
1.0
I03
Diamond
0.97630
SYNCHROTRON
DIAMOND BEAMLINE I03
32662.479
SERINE/THREONINE-PROTEIN KINASE NEK2
2.7.11.1
KINASE DOMAIN, RESIDUES 1-271
1
man
polymer
538.561
4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE
1
syn
non-polymer
35.453
CHLORIDE ION
4
syn
non-polymer
62.068
1,2-ETHANEDIOL
5
syn
non-polymer
18.015
water
224
nat
water
NEVER IN MITOSIS A-RELATED KINASE 2, NEK2, NIMA-RELATED PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, HSPK 21
no
no
MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT
TLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDF
GLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRY
SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT
TLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDF
GLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRY
SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
HUMAN
sample
9606
HOMO SAPIENS
511693
ESCHERICHIA COLI
BL21
RIL
PET30
PLASMID
2.62
53.08
NONE
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2011-03-30
1
1
2011-05-08
1
2
2011-07-13
1
3
2023-12-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
STRUCTURE OF NEK2 BOUND TO CCT241734
HUMAN NEK2 KINASE ATPGAMMAS-BOUND
STRUCTURE OF NEK2 BOUND TO CCT241799
STRUCTURE OF NEK2 BOUND TO THE AMINOPYRIDINE CCT241950
HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND
STRUCTURE OF NEK2 BOUND TO
STRUCTURE OF NEK2 BOUND TO CCT242101
STRUCTURE OF NEK2 BOUND TO CCT244744
HUMAN NEK2 KINASE ADP-BOUND
STRUCTURE OF NEK2 BOUND TO CCT193788
STRUCTURE OF NEK2 BOUND TO CCT242010
HUMAN NEK2 KINASE APO
STRUCTURE OF NEK2 BOUND TO CCT231393
STRUCTURE OF NEK2 BOUND TO CCT134934
STRUCTURE OF NEK2 BOUND TO CCT242430
STRUCTURE OF NEK2 BOUND TO CCT
STRUCTURE OF NEK2 BOUND TO CCT243779
PDBE
Y
PDBE
2010-08-05
REL
REL
1
A
O
HOH
2001
6.15
1
A
O
HOH
2002
6.08
1
A
O
HOH
2017
6.74
WCX
4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE
CL
CHLORIDE ION
EDO
1,2-ETHANEDIOL
HOH
water
2W5A
PDB ENTRY 2W5A
PDB
experimental model
WCX
1280
2
WCX
WCX
1280
A
CL
1281
3
CL
CL
1281
A
CL
1282
3
CL
CL
1282
A
CL
1283
3
CL
CL
1283
A
EDO
1284
4
EDO
EDO
1284
A
EDO
1285
4
EDO
EDO
1285
A
EDO
1286
4
EDO
EDO
1286
A
EDO
1287
4
EDO
EDO
1287
A
CL
1288
3
CL
CL
1288
A
EDO
1289
4
EDO
EDO
1289
A
HOH
2001
5
HOH
HOH
2001
A
HOH
2002
5
HOH
HOH
2002
A
HOH
2003
5
HOH
HOH
2003
A
HOH
2004
5
HOH
HOH
2004
A
HOH
2005
5
HOH
HOH
2005
A
HOH
2006
5
HOH
HOH
2006
A
HOH
2007
5
HOH
HOH
2007
A
HOH
2008
5
HOH
HOH
2008
A
HOH
2009
5
HOH
HOH
2009
A
HOH
2010
5
HOH
HOH
2010
A
HOH
2011
5
HOH
HOH
2011
A
HOH
2012
5
HOH
HOH
2012
A
HOH
2013
5
HOH
HOH
2013
A
HOH
2014
5
HOH
HOH
2014
A
HOH
2015
5
HOH
HOH
2015
A
HOH
2016
5
HOH
HOH
2016
A
HOH
2017
5
HOH
HOH
2017
A
HOH
2018
5
HOH
HOH
2018
A
HOH
2019
5
HOH
HOH
2019
A
HOH
2020
5
HOH
HOH
2020
A
HOH
2021
5
HOH
HOH
2021
A
HOH
2022
5
HOH
HOH
2022
A
HOH
2023
5
HOH
HOH
2023
A
HOH
2024
5
HOH
HOH
2024
A
HOH
2025
5
HOH
HOH
2025
A
HOH
2026
5
HOH
HOH
2026
A
HOH
2027
5
HOH
HOH
2027
A
HOH
2028
5
HOH
HOH
2028
A
HOH
2029
5
HOH
HOH
2029
A
HOH
2030
5
HOH
HOH
2030
A
HOH
2031
5
HOH
HOH
2031
A
HOH
2032
5
HOH
HOH
2032
A
HOH
2033
5
HOH
HOH
2033
A
HOH
2034
5
HOH
HOH
2034
A
HOH
2035
5
HOH
HOH
2035
A
HOH
2036
5
HOH
HOH
2036
A
HOH
2037
5
HOH
HOH
2037
A
HOH
2038
5
HOH
HOH
2038
A
HOH
2039
5
HOH
HOH
2039
A
HOH
2040
5
HOH
HOH
2040
A
HOH
2041
5
HOH
HOH
2041
A
HOH
2042
5
HOH
HOH
2042
A
HOH
2043
5
HOH
HOH
2043
A
HOH
2044
5
HOH
HOH
2044
A
HOH
2045
5
HOH
HOH
2045
A
HOH
2046
5
HOH
HOH
2046
A
HOH
2047
5
HOH
HOH
2047
A
HOH
2048
5
HOH
HOH
2048
A
HOH
2049
5
HOH
HOH
2049
A
HOH
2050
5
HOH
HOH
2050
A
HOH
2051
5
HOH
HOH
2051
A
HOH
2052
5
HOH
HOH
2052
A
HOH
2053
5
HOH
HOH
2053
A
HOH
2054
5
HOH
HOH
2054
A
HOH
2055
5
HOH
HOH
2055
A
HOH
2056
5
HOH
HOH
2056
A
HOH
2057
5
HOH
HOH
2057
A
HOH
2058
5
HOH
HOH
2058
A
HOH
2059
5
HOH
HOH
2059
A
HOH
2060
5
HOH
HOH
2060
A
HOH
2061
5
HOH
HOH
2061
A
HOH
2062
5
HOH
HOH
2062
A
HOH
2063
5
HOH
HOH
2063
A
HOH
2064
5
HOH
HOH
2064
A
HOH
2065
5
HOH
HOH
2065
A
HOH
2066
5
HOH
HOH
2066
A
HOH
2067
5
HOH
HOH
2067
A
HOH
2068
5
HOH
HOH
2068
A
HOH
2069
5
HOH
HOH
2069
A
HOH
2070
5
HOH
HOH
2070
A
HOH
2071
5
HOH
HOH
2071
A
HOH
2072
5
HOH
HOH
2072
A
HOH
2073
5
HOH
HOH
2073
A
HOH
2074
5
HOH
HOH
2074
A
HOH
2075
5
HOH
HOH
2075
A
HOH
2076
5
HOH
HOH
2076
A
HOH
2077
5
HOH
HOH
2077
A
HOH
2078
5
HOH
HOH
2078
A
HOH
2079
5
HOH
HOH
2079
A
HOH
2080
5
HOH
HOH
2080
A
HOH
2081
5
HOH
HOH
2081
A
HOH
2082
5
HOH
HOH
2082
A
HOH
2083
5
HOH
HOH
2083
A
HOH
2084
5
HOH
HOH
2084
A
HOH
2085
5
HOH
HOH
2085
A
HOH
2086
5
HOH
HOH
2086
A
HOH
2087
5
HOH
HOH
2087
A
HOH
2088
5
HOH
HOH
2088
A
HOH
2089
5
HOH
HOH
2089
A
HOH
2090
5
HOH
HOH
2090
A
HOH
2091
5
HOH
HOH
2091
A
HOH
2092
5
HOH
HOH
2092
A
HOH
2093
5
HOH
HOH
2093
A
HOH
2094
5
HOH
HOH
2094
A
HOH
2095
5
HOH
HOH
2095
A
HOH
2096
5
HOH
HOH
2096
A
HOH
2097
5
HOH
HOH
2097
A
HOH
2098
5
HOH
HOH
2098
A
HOH
2099
5
HOH
HOH
2099
A
HOH
2100
5
HOH
HOH
2100
A
HOH
2101
5
HOH
HOH
2101
A
HOH
2102
5
HOH
HOH
2102
A
HOH
2103
5
HOH
HOH
2103
A
HOH
2104
5
HOH
HOH
2104
A
HOH
2105
5
HOH
HOH
2105
A
HOH
2106
5
HOH
HOH
2106
A
HOH
2107
5
HOH
HOH
2107
A
HOH
2108
5
HOH
HOH
2108
A
HOH
2109
5
HOH
HOH
2109
A
HOH
2110
5
HOH
HOH
2110
A
HOH
2111
5
HOH
HOH
2111
A
HOH
2112
5
HOH
HOH
2112
A
HOH
2113
5
HOH
HOH
2113
A
HOH
2114
5
HOH
HOH
2114
A
HOH
2115
5
HOH
HOH
2115
A
HOH
2116
5
HOH
HOH
2116
A
HOH
2117
5
HOH
HOH
2117
A
HOH
2118
5
HOH
HOH
2118
A
HOH
2119
5
HOH
HOH
2119
A
HOH
2120
5
HOH
HOH
2120
A
HOH
2121
5
HOH
HOH
2121
A
HOH
2122
5
HOH
HOH
2122
A
HOH
2123
5
HOH
HOH
2123
A
HOH
2124
5
HOH
HOH
2124
A
HOH
2125
5
HOH
HOH
2125
A
HOH
2126
5
HOH
HOH
2126
A
HOH
2127
5
HOH
HOH
2127
A
HOH
2128
5
HOH
HOH
2128
A
HOH
2129
5
HOH
HOH
2129
A
HOH
2130
5
HOH
HOH
2130
A
HOH
2131
5
HOH
HOH
2131
A
HOH
2132
5
HOH
HOH
2132
A
HOH
2133
5
HOH
HOH
2133
A
HOH
2134
5
HOH
HOH
2134
A
HOH
2135
5
HOH
HOH
2135
A
HOH
2136
5
HOH
HOH
2136
A
HOH
2137
5
HOH
HOH
2137
A
HOH
2138
5
HOH
HOH
2138
A
HOH
2139
5
HOH
HOH
2139
A
HOH
2140
5
HOH
HOH
2140
A
HOH
2141
5
HOH
HOH
2141
A
HOH
2142
5
HOH
HOH
2142
A
HOH
2143
5
HOH
HOH
2143
A
HOH
2144
5
HOH
HOH
2144
A
HOH
2145
5
HOH
HOH
2145
A
HOH
2146
5
HOH
HOH
2146
A
HOH
2147
5
HOH
HOH
2147
A
HOH
2148
5
HOH
HOH
2148
A
HOH
2149
5
HOH
HOH
2149
A
HOH
2150
5
HOH
HOH
2150
A
HOH
2151
5
HOH
HOH
2151
A
HOH
2152
5
HOH
HOH
2152
A
HOH
2153
5
HOH
HOH
2153
A
HOH
2154
5
HOH
HOH
2154
A
HOH
2155
5
HOH
HOH
2155
A
HOH
2156
5
HOH
HOH
2156
A
HOH
2157
5
HOH
HOH
2157
A
HOH
2158
5
HOH
HOH
2158
A
HOH
2159
5
HOH
HOH
2159
A
HOH
2160
5
HOH
HOH
2160
A
HOH
2161
5
HOH
HOH
2161
A
HOH
2162
5
HOH
HOH
2162
A
HOH
2163
5
HOH
HOH
2163
A
HOH
2164
5
HOH
HOH
2164
A
HOH
2165
5
HOH
HOH
2165
A
HOH
2166
5
HOH
HOH
2166
A
HOH
2167
5
HOH
HOH
2167
A
HOH
2168
5
HOH
HOH
2168
A
HOH
2169
5
HOH
HOH
2169
A
HOH
2170
5
HOH
HOH
2170
A
HOH
2171
5
HOH
HOH
2171
A
HOH
2172
5
HOH
HOH
2172
A
HOH
2173
5
HOH
HOH
2173
A
HOH
2174
5
HOH
HOH
2174
A
HOH
2175
5
HOH
HOH
2175
A
HOH
2176
5
HOH
HOH
2176
A
HOH
2177
5
HOH
HOH
2177
A
HOH
2178
5
HOH
HOH
2178
A
HOH
2179
5
HOH
HOH
2179
A
HOH
2180
5
HOH
HOH
2180
A
HOH
2181
5
HOH
HOH
2181
A
HOH
2182
5
HOH
HOH
2182
A
HOH
2183
5
HOH
HOH
2183
A
HOH
2184
5
HOH
HOH
2184
A
HOH
2185
5
HOH
HOH
2185
A
HOH
2186
5
HOH
HOH
2186
A
HOH
2187
5
HOH
HOH
2187
A
HOH
2188
5
HOH
HOH
2188
A
HOH
2189
5
HOH
HOH
2189
A
HOH
2190
5
HOH
HOH
2190
A
HOH
2191
5
HOH
HOH
2191
A
HOH
2192
5
HOH
HOH
2192
A
HOH
2193
5
HOH
HOH
2193
A
HOH
2194
5
HOH
HOH
2194
A
HOH
2195
5
HOH
HOH
2195
A
HOH
2196
5
HOH
HOH
2196
A
HOH
2197
5
HOH
HOH
2197
A
HOH
2198
5
HOH
HOH
2198
A
HOH
2199
5
HOH
HOH
2199
A
HOH
2200
5
HOH
HOH
2200
A
HOH
2201
5
HOH
HOH
2201
A
HOH
2202
5
HOH
HOH
2202
A
HOH
2203
5
HOH
HOH
2203
A
HOH
2204
5
HOH
HOH
2204
A
HOH
2205
5
HOH
HOH
2205
A
HOH
2206
5
HOH
HOH
2206
A
HOH
2207
5
HOH
HOH
2207
A
HOH
2208
5
HOH
HOH
2208
A
HOH
2209
5
HOH
HOH
2209
A
HOH
2210
5
HOH
HOH
2210
A
HOH
2211
5
HOH
HOH
2211
A
HOH
2212
5
HOH
HOH
2212
A
HOH
2213
5
HOH
HOH
2213
A
HOH
2214
5
HOH
HOH
2214
A
HOH
2215
5
HOH
HOH
2215
A
HOH
2216
5
HOH
HOH
2216
A
HOH
2217
5
HOH
HOH
2217
A
HOH
2218
5
HOH
HOH
2218
A
HOH
2219
5
HOH
HOH
2219
A
HOH
2220
5
HOH
HOH
2220
A
HOH
2221
5
HOH
HOH
2221
A
HOH
2222
5
HOH
HOH
2222
A
HOH
2223
5
HOH
HOH
2223
A
HOH
2224
5
HOH
HOH
2224
A
n
1
1
A
n
2
2
A
SER
3
n
3
SER
3
A
ARG
4
n
4
ARG
4
A
ALA
5
n
5
ALA
5
A
GLU
6
n
6
GLU
6
A
ASP
7
n
7
ASP
7
A
TYR
8
n
8
TYR
8
A
GLU
9
n
9
GLU
9
A
VAL
10
n
10
VAL
10
A
LEU
11
n
11
LEU
11
A
TYR
12
n
12
TYR
12
A
THR
13
n
13
THR
13
A
ILE
14
n
14
ILE
14
A
GLY
15
n
15
GLY
15
A
THR
16
n
16
THR
16
A
GLY
17
n
17
GLY
17
A
n
18
18
A
TYR
19
n
19
TYR
19
A
GLY
20
n
20
GLY
20
A
ARG
21
n
21
ARG
21
A
CYS
22
n
22
CYS
22
A
GLN
23
n
23
GLN
23
A
LYS
24
n
24
LYS
24
A
ILE
25
n
25
ILE
25
A
ARG
26
n
26
ARG
26
A
ARG
27
n
27
ARG
27
A
LYS
28
n
28
LYS
28
A
SER
29
n
29
SER
29
A
ASP
30
n
30
ASP
30
A
GLY
31
n
31
GLY
31
A
LYS
32
n
32
LYS
32
A
ILE
33
n
33
ILE
33
A
LEU
34
n
34
LEU
34
A
VAL
35
n
35
VAL
35
A
TRP
36
n
36
TRP
36
A
LYS
37
n
37
LYS
37
A
GLU
38
n
38
GLU
38
A
LEU
39
n
39
LEU
39
A
ASP
40
n
40
ASP
40
A
TYR
41
n
41
TYR
41
A
GLY
42
n
42
GLY
42
A
SER
43
n
43
SER
43
A
MET
44
n
44
MET
44
A
THR
45
n
45
THR
45
A
GLU
46
n
46
GLU
46
A
ALA
47
n
47
ALA
47
A
GLU
48
n
48
GLU
48
A
LYS
49
n
49
LYS
49
A
GLN
50
n
50
GLN
50
A
MET
51
n
51
MET
51
A
LEU
52
n
52
LEU
52
A
VAL
53
n
53
VAL
53
A
SER
54
n
54
SER
54
A
GLU
55
n
55
GLU
55
A
VAL
56
n
56
VAL
56
A
ASN
57
n
57
ASN
57
A
LEU
58
n
58
LEU
58
A
LEU
59
n
59
LEU
59
A
ARG
60
n
60
ARG
60
A
GLU
61
n
61
GLU
61
A
LEU
62
n
62
LEU
62
A
LYS
63
n
63
LYS
63
A
HIS
64
n
64
HIS
64
A
PRO
65
n
65
PRO
65
A
ASN
66
n
66
ASN
66
A
ILE
67
n
67
ILE
67
A
VAL
68
n
68
VAL
68
A
ARG
69
n
69
ARG
69
A
TYR
70
n
70
TYR
70
A
TYR
71
n
71
TYR
71
A
ASP
72
n
72
ASP
72
A
ARG
73
n
73
ARG
73
A
ILE
74
n
74
ILE
74
A
ILE
75
n
75
ILE
75
A
ASP
76
n
76
ASP
76
A
ARG
77
n
77
ARG
77
A
THR
78
n
78
THR
78
A
ASN
79
n
79
ASN
79
A
THR
80
n
80
THR
80
A
THR
81
n
81
THR
81
A
LEU
82
n
82
LEU
82
A
TYR
83
n
83
TYR
83
A
ILE
84
n
84
ILE
84
A
VAL
85
n
85
VAL
85
A
MET
86
n
86
MET
86
A
GLU
87
n
87
GLU
87
A
TYR
88
n
88
TYR
88
A
CYS
89
n
89
CYS
89
A
GLU
90
n
90
GLU
90
A
GLY
91
n
91
GLY
91
A
GLY
92
n
92
GLY
92
A
ASP
93
n
93
ASP
93
A
LEU
94
n
94
LEU
94
A
ALA
95
n
95
ALA
95
A
SER
96
n
96
SER
96
A
VAL
97
n
97
VAL
97
A
ILE
98
n
98
ILE
98
A
THR
99
n
99
THR
99
A
LYS
100
n
100
LYS
100
A
GLY
101
n
101
GLY
101
A
THR
102
n
102
THR
102
A
LYS
103
n
103
LYS
103
A
GLU
104
n
104
GLU
104
A
ARG
105
n
105
ARG
105
A
GLN
106
n
106
GLN
106
A
TYR
107
n
107
TYR
107
A
LEU
108
n
108
LEU
108
A
ASP
109
n
109
ASP
109
A
GLU
110
n
110
GLU
110
A
GLU
111
n
111
GLU
111
A
PHE
112
n
112
PHE
112
A
VAL
113
n
113
VAL
113
A
LEU
114
n
114
LEU
114
A
ARG
115
n
115
ARG
115
A
VAL
116
n
116
VAL
116
A
MET
117
n
117
MET
117
A
THR
118
n
118
THR
118
A
GLN
119
n
119
GLN
119
A
LEU
120
n
120
LEU
120
A
THR
121
n
121
THR
121
A
LEU
122
n
122
LEU
122
A
ALA
123
n
123
ALA
123
A
LEU
124
n
124
LEU
124
A
LYS
125
n
125
LYS
125
A
GLU
126
n
126
GLU
126
A
CYS
127
n
127
CYS
127
A
HIS
128
n
128
HIS
128
A
ARG
129
n
129
ARG
129
A
ARG
130
n
130
ARG
130
A
SER
131
n
131
SER
131
A
n
132
132
A
n
133
133
A
n
134
134
A
n
135
135
A
n
136
136
A
n
137
137
A
n
138
138
A
HIS
139
n
139
HIS
139
A
ARG
140
n
140
ARG
140
A
ASP
141
n
141
ASP
141
A
LEU
142
n
142
LEU
142
A
LYS
143
n
143
LYS
143
A
PRO
144
n
144
PRO
144
A
ALA
145
n
145
ALA
145
A
ASN
146
n
146
ASN
146
A
VAL
147
n
147
VAL
147
A
PHE
148
n
148
PHE
148
A
LEU
149
n
149
LEU
149
A
ASP
150
n
150
ASP
150
A
GLY
151
n
151
GLY
151
A
LYS
152
n
152
LYS
152
A
GLN
153
n
153
GLN
153
A
ASN
154
n
154
ASN
154
A
VAL
155
n
155
VAL
155
A
LYS
156
n
156
LYS
156
A
LEU
157
n
157
LEU
157
A
GLY
158
n
158
GLY
158
A
ASP
159
n
159
ASP
159
A
PHE
160
n
160
PHE
160
A
GLY
161
n
161
GLY
161
A
LEU
162
n
162
LEU
162
A
n
163
163
A
n
164
164
A
n
165
165
A
n
166
166
A
n
167
167
A
n
168
168
A
n
169
169
A
n
170
170
A
n
171
171
A
n
172
172
A
n
173
173
A
n
174
174
A
n
175
175
A
PHE
176
n
176
PHE
176
A
VAL
177
n
177
VAL
177
A
GLY
178
n
178
GLY
178
A
THR
179
n
179
THR
179
A
PRO
180
n
180
PRO
180
A
TYR
181
n
181
TYR
181
A
TYR
182
n
182
TYR
182
A
MET
183
n
183
MET
183
A
SER
184
n
184
SER
184
A
PRO
185
n
185
PRO
185
A
GLU
186
n
186
GLU
186
A
GLN
187
n
187
GLN
187
A
MET
188
n
188
MET
188
A
ASN
189
n
189
ASN
189
A
ARG
190
n
190
ARG
190
A
n
191
191
A
n
192
192
A
n
193
193
A
ASN
194
n
194
ASN
194
A
GLU
195
n
195
GLU
195
A
LYS
196
n
196
LYS
196
A
SER
197
n
197
SER
197
A
ASP
198
n
198
ASP
198
A
ILE
199
n
199
ILE
199
A
TRP
200
n
200
TRP
200
A
SER
201
n
201
SER
201
A
LEU
202
n
202
LEU
202
A
GLY
203
n
203
GLY
203
A
CYS
204
n
204
CYS
204
A
LEU
205
n
205
LEU
205
A
LEU
206
n
206
LEU
206
A
TYR
207
n
207
TYR
207
A
GLU
208
n
208
GLU
208
A
LEU
209
n
209
LEU
209
A
CYS
210
n
210
CYS
210
A
ALA
211
n
211
ALA
211
A
LEU
212
n
212
LEU
212
A
MET
213
n
213
MET
213
A
PRO
214
n
214
PRO
214
A
PRO
215
n
215
PRO
215
A
PHE
216
n
216
PHE
216
A
THR
217
n
217
THR
217
A
ALA
218
n
218
ALA
218
A
PHE
219
n
219
PHE
219
A
SER
220
n
220
SER
220
A
GLN
221
n
221
GLN
221
A
LYS
222
n
222
LYS
222
A
GLU
223
n
223
GLU
223
A
LEU
224
n
224
LEU
224
A
ALA
225
n
225
ALA
225
A
GLY
226
n
226
GLY
226
A
LYS
227
n
227
LYS
227
A
ILE
228
n
228
ILE
228
A
ARG
229
n
229
ARG
229
A
GLU
230
n
230
GLU
230
A
GLY
231
n
231
GLY
231
A
LYS
232
n
232
LYS
232
A
PHE
233
n
233
PHE
233
A
ARG
234
n
234
ARG
234
A
ARG
235
n
235
ARG
235
A
ILE
236
n
236
ILE
236
A
PRO
237
n
237
PRO
237
A
TYR
238
n
238
TYR
238
A
ARG
239
n
239
ARG
239
A
TYR
240
n
240
TYR
240
A
SER
241
n
241
SER
241
A
ASP
242
n
242
ASP
242
A
GLU
243
n
243
GLU
243
A
LEU
244
n
244
LEU
244
A
ASN
245
n
245
ASN
245
A
GLU
246
n
246
GLU
246
A
ILE
247
n
247
ILE
247
A
ILE
248
n
248
ILE
248
A
THR
249
n
249
THR
249
A
ARG
250
n
250
ARG
250
A
MET
251
n
251
MET
251
A
LEU
252
n
252
LEU
252
A
ASN
253
n
253
ASN
253
A
LEU
254
n
254
LEU
254
A
LYS
255
n
255
LYS
255
A
ASP
256
n
256
ASP
256
A
TYR
257
n
257
TYR
257
A
HIS
258
n
258
HIS
258
A
ARG
259
n
259
ARG
259
A
PRO
260
n
260
PRO
260
A
SER
261
n
261
SER
261
A
VAL
262
n
262
VAL
262
A
GLU
263
n
263
GLU
263
A
GLU
264
n
264
GLU
264
A
ILE
265
n
265
ILE
265
A
LEU
266
n
266
LEU
266
A
GLU
267
n
267
GLU
267
A
ASN
268
n
268
ASN
268
A
PRO
269
n
269
PRO
269
A
LEU
270
n
270
LEU
270
A
ILE
271
n
271
ILE
271
A
LEU
272
n
272
LEU
272
A
GLU
273
n
273
GLU
273
A
HIS
274
n
274
HIS
274
A
HIS
275
n
275
HIS
275
A
HIS
276
n
276
HIS
276
A
HIS
277
n
277
HIS
277
A
HIS
278
n
278
HIS
278
A
HIS
279
n
279
HIS
279
A
1.8964
-0.4079
1.3599
1.0719
0.2560
1.6145
0.0589
0.6825
-0.4494
-0.1658
0.0379
0.3849
0.0500
0.1922
-0.0523
0.1079
-0.0168
-0.0551
0.2812
-0.0929
0.1845
refined
-29.4606
-10.8542
10.1849
X-RAY DIFFRACTION
1.6984
1.0032
0.1542
1.1304
0.0112
0.0328
-0.0113
0.1989
0.1334
-0.0364
0.0209
0.1336
0.0430
-0.0656
0.0021
0.0420
-0.0053
0.0023
0.0880
0.0001
0.0378
refined
-18.1899
-3.5685
20.2085
X-RAY DIFFRACTION
0.9834
0.5889
-0.2228
1.2230
0.2581
0.5304
-0.0868
0.1713
0.0150
-0.0726
0.0519
-0.0260
-0.0771
-0.0708
0.0308
0.0547
-0.0074
0.0068
0.0560
0.0039
0.0269
refined
-6.0602
9.0524
19.3764
X-RAY DIFFRACTION
1.8860
0.5218
-2.1642
0.8693
-0.2244
5.1072
-0.2707
0.3876
0.3113
0.0362
0.0819
0.0659
-0.0430
-0.4241
0.1546
0.1081
-0.0013
-0.0086
0.1657
0.0510
0.1712
refined
-26.4379
-2.4046
18.7578
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
(CHAIN A AND RESID 3:63)
X-RAY DIFFRACTION
2
(CHAIN A AND RESID 64:157)
X-RAY DIFFRACTION
3
(CHAIN A AND RESID 158:279)
X-RAY DIFFRACTION
4
(CHAIN A AND RESID 1280)
software_defined_assembly
PISA
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ILE
14
A
N
ILE
14
A
O
CYS
22
A
O
CYS
22
A
N
ILE
25
A
N
ILE
25
A
O
LEU
34
A
O
LEU
34
A
N
LEU
39
A
N
LEU
39
A
O
LEU
82
A
O
LEU
82
A
O
VAL
85
A
O
VAL
85
A
N
TYR
71
A
N
TYR
71
A
O
GLY
92
A
O
GLY
92
A
N
LEU
149
A
N
LEU
149
A
N
PHE
148
A
N
PHE
148
A
O
LYS
156
A
O
LYS
156
1
A
HOH
2080
L
HOH
1
A
CA
SER
54
A
CA
SER
54
0
Y
1
A
CD
ARG
69
A
CD
ARG
69
0
Y
1
A
NH2
ARG
69
A
NH2
ARG
69
0
Y
1
A
CG
ARG
77
A
CG
ARG
77
1
Y
1
A
CD
ARG
77
A
CD
ARG
77
1
Y
1
A
NE
ARG
77
A
NE
ARG
77
1
Y
1
A
CZ
ARG
77
A
CZ
ARG
77
1
Y
1
A
NH1
ARG
77
A
NH1
ARG
77
1
Y
1
A
NH2
ARG
77
A
NH2
ARG
77
1
Y
1
A
CG
ASN
79
A
CG
ASN
79
1
Y
1
A
OD1
ASN
79
A
OD1
ASN
79
1
Y
1
A
ND2
ASN
79
A
ND2
ASN
79
1
Y
1
A
NE
ARG
130
A
NE
ARG
130
1
Y
1
A
CZ
ARG
130
A
CZ
ARG
130
1
Y
1
A
NH1
ARG
130
A
NH1
ARG
130
1
Y
1
A
NH2
ARG
130
A
NH2
ARG
130
1
Y
1
A
CG
HIS
139
A
CG
HIS
139
1
Y
1
A
ND1
HIS
139
A
ND1
HIS
139
1
Y
1
A
CD2
HIS
139
A
CD2
HIS
139
1
Y
1
A
CE1
HIS
139
A
CE1
HIS
139
1
Y
1
A
NE2
HIS
139
A
NE2
HIS
139
1
Y
1
A
CG
MET
188
A
CG
MET
188
0
Y
1
A
OE1
GLN
221
A
OE1
GLN
221
0
Y
1
A
MET
1
A
MET
1
1
Y
1
A
PRO
2
A
PRO
2
1
Y
1
A
SER
18
A
SER
18
1
Y
1
A
ASP
132
A
ASP
132
1
Y
1
A
GLY
133
A
GLY
133
1
Y
1
A
GLY
134
A
GLY
134
1
Y
1
A
HIS
135
A
HIS
135
1
Y
1
A
THR
136
A
THR
136
1
Y
1
A
VAL
137
A
VAL
137
1
Y
1
A
LEU
138
A
LEU
138
1
Y
1
A
ALA
163
A
ALA
163
1
Y
1
A
ARG
164
A
ARG
164
1
Y
1
A
ILE
165
A
ILE
165
1
Y
1
A
LEU
166
A
LEU
166
1
Y
1
A
ASN
167
A
ASN
167
1
Y
1
A
HIS
168
A
HIS
168
1
Y
1
A
ASP
169
A
ASP
169
1
Y
1
A
THR
170
A
THR
170
1
Y
1
A
SER
171
A
SER
171
1
Y
1
A
PHE
172
A
PHE
172
1
Y
1
A
ALA
173
A
ALA
173
1
Y
1
A
LYS
174
A
LYS
174
1
Y
1
A
THR
175
A
THR
175
1
Y
1
A
MET
191
A
MET
191
1
Y
1
A
SER
192
A
SER
192
1
Y
1
A
TYR
193
A
TYR
193
1
Y
1
A
ASP
76
-103.40
79.12
1
A
THR
80
38.21
52.00
1
A
MET
188
-49.96
-19.30
1
A
ASN
189
-142.50
-28.00
30.82
-1.0725
-0.0000
-6.3588
-4.8910
0.0000
5.9635
0.2012
0.1566
0.1589
1.98
36.784
1165
22973
5.1
96.84
0.21
1
0.03
MOLECULAR REPLACEMENT
18.79
0.90
1.11
PDB ENTRY 2W5A
ML
FLAT BULK SOLVENT MODEL
60.124
0.346
1.98
36.784
224
2362
63
0
2075
0.010
2203
1.212
2966
19.784
860
0.087
317
0.005
371
0.2100
0.1690
2.0701
157
2625
94.00
0.2256
0.1621
2.1792
143
2638
95.00
0.2052
0.1483
2.3158
134
2690
96.00
0.1766
0.1449
2.4945
117
2745
97.00
0.2085
0.1462
2.7455
145
2750
97.00
0.2193
0.1488
3.1426
149
2769
99.00
0.1816
0.1449
3.9586
138
2789
99.00
0.1908
0.1670
36.7904
182
2802
98.00
18.50
1.90
46.52
2XNP
26646
6.0
0.06
1
11.10
3.6
99.4
0.40
1.90
2.00
2.50
1
3.6
99.7
refinement
PHENIX
(PHENIX.REFINE)
data reduction
MOSFLM
data scaling
SCALA
phasing
PHASER
Structure of Nek2 bound to CCT244858
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
3
N
N
4
N
N
5
N
N
A
ARG
4
A
ARG
4
HELX_P
A
GLU
6
A
GLU
6
5
1
3
A
THR
45
A
THR
45
HELX_P
A
GLU
61
A
GLU
61
1
2
17
A
LEU
94
A
LEU
94
HELX_P
A
ARG
105
A
ARG
105
1
3
12
A
ASP
109
A
ASP
109
HELX_P
A
SER
131
A
SER
131
1
4
23
A
LYS
143
A
LYS
143
HELX_P
A
ALA
145
A
ALA
145
5
5
3
A
ASN
194
A
ASN
194
HELX_P
A
LEU
212
A
LEU
212
1
6
19
A
SER
220
A
SER
220
HELX_P
A
GLY
231
A
GLY
231
1
7
12
A
SER
241
A
SER
241
HELX_P
A
LEU
252
A
LEU
252
1
8
12
A
LYS
255
A
LYS
255
HELX_P
A
ARG
259
A
ARG
259
5
9
5
A
SER
261
A
SER
261
HELX_P
A
GLU
267
A
GLU
267
1
10
7
A
LEU
272
A
LEU
272
HELX_P
A
HIS
276
A
HIS
276
5
11
5
TRANSFERASE
TRANSFERASE, CENTROSOME, MITOSIS, CELL CYCLE
NEK2_HUMAN
UNP
1
P51955
1
271
2XNP
1
271
P51955
A
1
1
271
1
expression tag
LEU
272
2XNP
A
P51955
UNP
272
1
expression tag
GLU
273
2XNP
A
P51955
UNP
273
1
expression tag
HIS
274
2XNP
A
P51955
UNP
274
1
expression tag
HIS
275
2XNP
A
P51955
UNP
275
1
expression tag
HIS
276
2XNP
A
P51955
UNP
276
1
expression tag
HIS
277
2XNP
A
P51955
UNP
277
1
expression tag
HIS
278
2XNP
A
P51955
UNP
278
1
expression tag
HIS
279
2XNP
A
P51955
UNP
279
5
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
8
A
TYR
8
A
THR
16
A
THR
16
A
ARG
21
A
ARG
21
A
ARG
27
A
ARG
27
A
ILE
33
A
ILE
33
A
ASP
40
A
ASP
40
A
THR
81
A
THR
81
A
GLU
87
A
GLU
87
A
TYR
70
A
TYR
70
A
ASP
76
A
ASP
76
A
GLY
92
A
GLY
92
A
ASP
93
A
ASP
93
A
VAL
147
A
VAL
147
A
LEU
149
A
LEU
149
A
VAL
155
A
VAL
155
A
LEU
157
A
LEU
157
BINDING SITE FOR RESIDUE WCX A 1280
A
WCX
1280
Software
16
BINDING SITE FOR RESIDUE CL A 1282
A
CL
1282
Software
4
BINDING SITE FOR RESIDUE CL A 1288
A
CL
1288
Software
1
BINDING SITE FOR RESIDUE CL A 1283
A
CL
1283
Software
4
BINDING SITE FOR RESIDUE EDO A 1284
A
EDO
1284
Software
6
BINDING SITE FOR RESIDUE EDO A 1285
A
EDO
1285
Software
6
BINDING SITE FOR RESIDUE EDO A 1286
A
EDO
1286
Software
5
BINDING SITE FOR RESIDUE EDO A 1287
A
EDO
1287
Software
6
BINDING SITE FOR RESIDUE EDO A 1289
A
EDO
1289
Software
6
A
ILE
14
A
ILE
14
16
1_555
A
GLY
15
A
GLY
15
16
1_555
A
TYR
19
A
TYR
19
16
1_555
A
CYS
22
A
CYS
22
16
1_555
A
GLU
87
A
GLU
87
16
1_555
A
TYR
88
A
TYR
88
16
1_555
A
CYS
89
A
CYS
89
16
1_555
A
GLU
90
A
GLU
90
16
1_555
A
GLY
92
A
GLY
92
16
1_555
A
ASP
93
A
ASP
93
16
1_555
A
ALA
145
A
ALA
145
16
1_555
A
PHE
148
A
PHE
148
16
1_555
A
GLY
158
A
GLY
158
16
1_555
A
ASP
159
A
ASP
159
16
1_555
A
PHE
160
A
PHE
160
16
1_555
A
HOH
2216
L
HOH
16
1_555
A
ASN
154
A
ASN
154
4
1_555
A
HIS
277
A
HIS
277
4
1_555
A
HIS
279
A
HIS
279
4
1_555
A
HOH
2132
L
HOH
4
1_555
A
HOH
2160
L
HOH
1
1_555
A
TYR
207
A
TYR
207
4
1_555
A
PRO
215
A
PRO
215
4
1_555
A
PHE
233
A
PHE
233
4
1_555
A
ARG
234
A
ARG
234
4
1_555
A
TYR
181
A
TYR
181
6
1_555
A
TYR
182
A
TYR
182
6
1_555
A
GLU
208
A
GLU
208
6
1_555
A
PRO
214
A
PRO
214
6
1_555
A
HOH
2217
L
HOH
6
1_555
A
HOH
2219
L
HOH
6
1_555
A
ASP
242
A
ASP
242
6
1_555
A
GLU
243
A
GLU
243
6
1_555
A
GLU
246
A
GLU
246
6
1_555
A
HIS
277
A
HIS
277
6
4_556
A
HIS
279
A
HIS
279
6
4_556
A
HOH
2220
L
HOH
6
1_555
A
LYS
152
A
LYS
152
5
1_555
A
GLN
153
A
GLN
153
5
1_555
A
HOH
2131
L
HOH
5
1_555
A
HOH
2214
L
HOH
5
1_555
A
HOH
2221
L
HOH
5
1_555
A
GLU
195
A
GLU
195
6
1_555
A
LYS
196
A
LYS
196
6
1_555
A
SER
261
A
SER
261
6
1_555
A
VAL
262
A
VAL
262
6
1_555
A
HOH
2117
L
HOH
6
1_555
A
HOH
2200
L
HOH
6
1_555
A
ARG
234
A
ARG
234
6
4_546
A
ARG
235
A
ARG
235
6
4_546
A
LEU
266
A
LEU
266
6
1_555
A
HOH
2166
L
HOH
6
4_546
A
HOH
2222
L
HOH
6
1_555
A
HOH
2224
L
HOH
6
1_555
5
C 1 2 1