0.010174
0.005874
0.000000
-0.000000
0.011748
0.000000
0.000000
-0.000000
0.012410
0.00000
0.00000
0.00000
Stoll, V.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
98.286
98.286
80.580
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
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
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C15 H14 Cl N3 O2 S
335.809
8-chloro-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzothieno[3,2-d]pyrimidin-4(3H)-one
non-polymer
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
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
N
N
159
S
C
N
160
N
C
N
161
N
O
N
162
S
C
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
N
N
181
S
C
N
182
N
C
N
183
N
O
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
S
C
N
203
N
N
N
204
N
O
Y
205
N
S
N
206
N
CL
N
207
N
C
N
208
N
N
N
209
N
O
N
210
N
C
N
211
N
N
N
212
N
C
N
213
N
C
Y
214
N
C
Y
215
N
C
Y
216
N
C
Y
217
N
C
Y
218
N
C
Y
219
N
C
Y
220
N
C
Y
221
N
C
N
222
N
C
N
223
N
C
N
224
N
H
N
225
N
H
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
N
N
239
S
C
N
240
N
C
N
241
N
O
N
242
N
C
N
243
N
C
N
244
N
C
N
245
N
C
N
246
N
N
N
247
N
O
N
248
N
H
N
249
N
H
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
H
N
262
N
H
N
263
N
N
N
264
S
C
N
265
N
C
N
266
N
O
N
267
N
C
N
268
N
C
N
269
N
S
N
270
N
C
N
271
N
O
N
272
N
H
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
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
Y
288
N
C
Y
289
N
C
Y
290
N
C
Y
291
N
C
Y
292
N
C
Y
293
N
C
N
294
N
O
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
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
N
N
307
S
C
N
308
N
C
N
309
N
O
N
310
N
C
N
311
N
C
N
312
N
C
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
N
C
N
328
N
O
N
329
N
O
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
R
C
N
342
N
O
N
343
N
C
N
344
N
O
N
345
N
H
N
346
N
H
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
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
N
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
N
368
N
O
N
369
N
H
N
370
N
H
N
371
N
H
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
N
N
382
S
C
N
383
N
C
N
384
N
O
N
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
N
392
N
O
N
393
N
O
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
H
N
403
N
H
N
404
N
H
N
405
N
N
N
406
S
C
N
407
N
C
N
408
N
O
N
409
N
C
N
410
N
C
N
411
N
C
N
412
N
O
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
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
doub
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
doub
N
98
N
sing
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
sing
N
107
N
sing
N
108
N
doub
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
doub
N
117
N
sing
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
sing
N
126
N
doub
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
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
doub
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
sing
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
doub
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
sing
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
Y
200
N
sing
Y
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
doub
N
208
N
doub
N
209
N
sing
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
Y
217
N
doub
Y
218
N
sing
Y
219
N
sing
Y
220
N
doub
Y
221
N
sing
N
222
N
sing
Y
223
N
doub
Y
224
N
sing
N
225
N
sing
Y
226
N
doub
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
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
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
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
doub
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
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
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
Y
285
N
doub
Y
286
N
sing
Y
287
N
sing
N
288
N
sing
Y
289
N
doub
N
290
N
sing
Y
291
N
doub
N
292
N
sing
Y
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
doub
N
304
N
sing
N
305
N
sing
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
doub
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
doub
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
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
Y
359
N
sing
Y
360
N
sing
N
361
N
sing
Y
362
N
sing
Y
363
N
doub
N
364
N
sing
Y
365
N
doub
N
366
N
sing
Y
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
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
doub
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
Y
382
N
doub
Y
383
N
sing
Y
384
N
sing
N
385
N
sing
Y
386
N
doub
N
387
N
sing
Y
388
N
doub
N
389
N
sing
Y
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
doub
N
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
N
411
N
sing
N
412
N
sing
To be Published
0353
Discovery of 3H-benzo[4,5]thieno[3,2-d]pyrimidin-4-ones as Potent, Highly Selective and Orally Bioavailable Pim Kinases Inhibitors
10.2210/pdb3jy0/pdb
pdb_00003jy0
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
MAR CCD 165 mm
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
17-BM
APS
1.0000
SYNCHROTRON
APS BEAMLINE 17-BM
33963.516
Proto-oncogene serine/threonine-protein kinase Pim-1
2.7.11.1
1
man
polymer
335.809
8-chloro-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzothieno[3,2-d]pyrimidin-4(3H)-one
1
syn
non-polymer
no
no
MKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLL
DWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDF
GSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLI
RWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSKVDHHHHHH
MKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLL
DWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDF
GSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLI
RWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSKVDHHHHHH
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
PIM1
9606
Homo sapiens
562
Escherichia coli
1
3.31
62.82
VAPOR DIFFUSION, HANGING DROP
VAPOR DIFFUSION, HANGING DROP, temperature 312K
312
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2009-11-10
1
1
2011-07-13
1
2
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Pim-1 structure of related chemical analog
RCSB
Y
RCSB
2009-09-21
REL
REL
LYG
8-chloro-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzothieno[3,2-d]pyrimidin-4(3H)-one
LYG
1000
2
LYG
LYG
1000
A
n
1
28
A
n
2
29
A
n
3
30
A
n
4
31
A
n
5
32
A
PRO
33
n
6
PRO
33
A
LEU
34
n
7
LEU
34
A
GLU
35
n
8
GLU
35
A
SER
36
n
9
SER
36
A
GLN
37
n
10
GLN
37
A
TYR
38
n
11
TYR
38
A
GLN
39
n
12
GLN
39
A
VAL
40
n
13
VAL
40
A
GLY
41
n
14
GLY
41
A
PRO
42
n
15
PRO
42
A
LEU
43
n
16
LEU
43
A
LEU
44
n
17
LEU
44
A
GLY
45
n
18
GLY
45
A
SER
46
n
19
SER
46
A
GLY
47
n
20
GLY
47
A
GLY
48
n
21
GLY
48
A
PHE
49
n
22
PHE
49
A
GLY
50
n
23
GLY
50
A
SER
51
n
24
SER
51
A
VAL
52
n
25
VAL
52
A
TYR
53
n
26
TYR
53
A
SER
54
n
27
SER
54
A
GLY
55
n
28
GLY
55
A
ILE
56
n
29
ILE
56
A
ARG
57
n
30
ARG
57
A
VAL
58
n
31
VAL
58
A
SER
59
n
32
SER
59
A
ASP
60
n
33
ASP
60
A
ASN
61
n
34
ASN
61
A
LEU
62
n
35
LEU
62
A
PRO
63
n
36
PRO
63
A
VAL
64
n
37
VAL
64
A
ALA
65
n
38
ALA
65
A
ILE
66
n
39
ILE
66
A
LYS
67
n
40
LYS
67
A
HIS
68
n
41
HIS
68
A
VAL
69
n
42
VAL
69
A
GLU
70
n
43
GLU
70
A
LYS
71
n
44
LYS
71
A
ASP
72
n
45
ASP
72
A
ARG
73
n
46
ARG
73
A
ILE
74
n
47
ILE
74
A
SER
75
n
48
SER
75
A
ASP
76
n
49
ASP
76
A
TRP
77
n
50
TRP
77
A
GLY
78
n
51
GLY
78
A
GLU
79
n
52
GLU
79
A
LEU
80
n
53
LEU
80
A
PRO
81
n
54
PRO
81
A
ASN
82
n
55
ASN
82
A
GLY
83
n
56
GLY
83
A
THR
84
n
57
THR
84
A
ARG
85
n
58
ARG
85
A
VAL
86
n
59
VAL
86
A
PRO
87
n
60
PRO
87
A
MET
88
n
61
MET
88
A
GLU
89
n
62
GLU
89
A
VAL
90
n
63
VAL
90
A
VAL
91
n
64
VAL
91
A
LEU
92
n
65
LEU
92
A
LEU
93
n
66
LEU
93
A
LYS
94
n
67
LYS
94
A
LYS
95
n
68
LYS
95
A
VAL
96
n
69
VAL
96
A
SER
97
n
70
SER
97
A
SER
98
n
71
SER
98
A
GLY
99
n
72
GLY
99
A
PHE
100
n
73
PHE
100
A
SER
101
n
74
SER
101
A
GLY
102
n
75
GLY
102
A
VAL
103
n
76
VAL
103
A
ILE
104
n
77
ILE
104
A
ARG
105
n
78
ARG
105
A
LEU
106
n
79
LEU
106
A
LEU
107
n
80
LEU
107
A
ASP
108
n
81
ASP
108
A
TRP
109
n
82
TRP
109
A
PHE
110
n
83
PHE
110
A
GLU
111
n
84
GLU
111
A
ARG
112
n
85
ARG
112
A
PRO
113
n
86
PRO
113
A
ASP
114
n
87
ASP
114
A
SER
115
n
88
SER
115
A
PHE
116
n
89
PHE
116
A
VAL
117
n
90
VAL
117
A
LEU
118
n
91
LEU
118
A
ILE
119
n
92
ILE
119
A
LEU
120
n
93
LEU
120
A
GLU
121
n
94
GLU
121
A
ARG
122
n
95
ARG
122
A
PRO
123
n
96
PRO
123
A
GLU
124
n
97
GLU
124
A
PRO
125
n
98
PRO
125
A
VAL
126
n
99
VAL
126
A
GLN
127
n
100
GLN
127
A
ASP
128
n
101
ASP
128
A
LEU
129
n
102
LEU
129
A
PHE
130
n
103
PHE
130
A
ASP
131
n
104
ASP
131
A
PHE
132
n
105
PHE
132
A
ILE
133
n
106
ILE
133
A
THR
134
n
107
THR
134
A
GLU
135
n
108
GLU
135
A
ARG
136
n
109
ARG
136
A
GLY
137
n
110
GLY
137
A
ALA
138
n
111
ALA
138
A
LEU
139
n
112
LEU
139
A
GLN
140
n
113
GLN
140
A
GLU
141
n
114
GLU
141
A
GLU
142
n
115
GLU
142
A
LEU
143
n
116
LEU
143
A
ALA
144
n
117
ALA
144
A
ARG
145
n
118
ARG
145
A
SER
146
n
119
SER
146
A
PHE
147
n
120
PHE
147
A
PHE
148
n
121
PHE
148
A
TRP
149
n
122
TRP
149
A
GLN
150
n
123
GLN
150
A
VAL
151
n
124
VAL
151
A
LEU
152
n
125
LEU
152
A
GLU
153
n
126
GLU
153
A
ALA
154
n
127
ALA
154
A
VAL
155
n
128
VAL
155
A
ARG
156
n
129
ARG
156
A
HIS
157
n
130
HIS
157
A
CYS
158
n
131
CYS
158
A
HIS
159
n
132
HIS
159
A
ASN
160
n
133
ASN
160
A
CYS
161
n
134
CYS
161
A
GLY
162
n
135
GLY
162
A
VAL
163
n
136
VAL
163
A
LEU
164
n
137
LEU
164
A
HIS
165
n
138
HIS
165
A
ARG
166
n
139
ARG
166
A
ASP
167
n
140
ASP
167
A
ILE
168
n
141
ILE
168
A
LYS
169
n
142
LYS
169
A
ASP
170
n
143
ASP
170
A
GLU
171
n
144
GLU
171
A
ASN
172
n
145
ASN
172
A
ILE
173
n
146
ILE
173
A
LEU
174
n
147
LEU
174
A
ILE
175
n
148
ILE
175
A
ASP
176
n
149
ASP
176
A
LEU
177
n
150
LEU
177
A
ASN
178
n
151
ASN
178
A
ARG
179
n
152
ARG
179
A
GLY
180
n
153
GLY
180
A
GLU
181
n
154
GLU
181
A
LEU
182
n
155
LEU
182
A
LYS
183
n
156
LYS
183
A
LEU
184
n
157
LEU
184
A
ILE
185
n
158
ILE
185
A
ASP
186
n
159
ASP
186
A
PHE
187
n
160
PHE
187
A
GLY
188
n
161
GLY
188
A
SER
189
n
162
SER
189
A
GLY
190
n
163
GLY
190
A
ALA
191
n
164
ALA
191
A
LEU
192
n
165
LEU
192
A
LEU
193
n
166
LEU
193
A
LYS
194
n
167
LYS
194
A
ASP
195
n
168
ASP
195
A
THR
196
n
169
THR
196
A
VAL
197
n
170
VAL
197
A
TYR
198
n
171
TYR
198
A
THR
199
n
172
THR
199
A
ASP
200
n
173
ASP
200
A
PHE
201
n
174
PHE
201
A
ASP
202
n
175
ASP
202
A
GLY
203
n
176
GLY
203
A
THR
204
n
177
THR
204
A
ARG
205
n
178
ARG
205
A
VAL
206
n
179
VAL
206
A
TYR
207
n
180
TYR
207
A
SER
208
n
181
SER
208
A
PRO
209
n
182
PRO
209
A
PRO
210
n
183
PRO
210
A
GLU
211
n
184
GLU
211
A
TRP
212
n
185
TRP
212
A
ILE
213
n
186
ILE
213
A
ARG
214
n
187
ARG
214
A
TYR
215
n
188
TYR
215
A
HIS
216
n
189
HIS
216
A
ARG
217
n
190
ARG
217
A
TYR
218
n
191
TYR
218
A
HIS
219
n
192
HIS
219
A
GLY
220
n
193
GLY
220
A
ARG
221
n
194
ARG
221
A
SER
222
n
195
SER
222
A
ALA
223
n
196
ALA
223
A
ALA
224
n
197
ALA
224
A
VAL
225
n
198
VAL
225
A
TRP
226
n
199
TRP
226
A
SER
227
n
200
SER
227
A
LEU
228
n
201
LEU
228
A
GLY
229
n
202
GLY
229
A
ILE
230
n
203
ILE
230
A
LEU
231
n
204
LEU
231
A
LEU
232
n
205
LEU
232
A
TYR
233
n
206
TYR
233
A
ASP
234
n
207
ASP
234
A
MET
235
n
208
MET
235
A
VAL
236
n
209
VAL
236
A
CYS
237
n
210
CYS
237
A
GLY
238
n
211
GLY
238
A
ASP
239
n
212
ASP
239
A
ILE
240
n
213
ILE
240
A
PRO
241
n
214
PRO
241
A
PHE
242
n
215
PHE
242
A
GLU
243
n
216
GLU
243
A
HIS
244
n
217
HIS
244
A
ASP
245
n
218
ASP
245
A
GLU
246
n
219
GLU
246
A
GLU
247
n
220
GLU
247
A
ILE
248
n
221
ILE
248
A
ILE
249
n
222
ILE
249
A
ARG
250
n
223
ARG
250
A
GLY
251
n
224
GLY
251
A
GLN
252
n
225
GLN
252
A
VAL
253
n
226
VAL
253
A
PHE
254
n
227
PHE
254
A
PHE
255
n
228
PHE
255
A
ARG
256
n
229
ARG
256
A
GLN
257
n
230
GLN
257
A
ARG
258
n
231
ARG
258
A
VAL
259
n
232
VAL
259
A
SER
260
n
233
SER
260
A
SER
261
n
234
SER
261
A
GLU
262
n
235
GLU
262
A
CYS
263
n
236
CYS
263
A
GLN
264
n
237
GLN
264
A
HIS
265
n
238
HIS
265
A
LEU
266
n
239
LEU
266
A
ILE
267
n
240
ILE
267
A
ARG
268
n
241
ARG
268
A
TRP
269
n
242
TRP
269
A
CYS
270
n
243
CYS
270
A
LEU
271
n
244
LEU
271
A
ALA
272
n
245
ALA
272
A
LEU
273
n
246
LEU
273
A
ARG
274
n
247
ARG
274
A
PRO
275
n
248
PRO
275
A
SER
276
n
249
SER
276
A
ASP
277
n
250
ASP
277
A
ARG
278
n
251
ARG
278
A
PRO
279
n
252
PRO
279
A
THR
280
n
253
THR
280
A
PHE
281
n
254
PHE
281
A
GLU
282
n
255
GLU
282
A
GLU
283
n
256
GLU
283
A
ILE
284
n
257
ILE
284
A
GLN
285
n
258
GLN
285
A
ASN
286
n
259
ASN
286
A
HIS
287
n
260
HIS
287
A
PRO
288
n
261
PRO
288
A
TRP
289
n
262
TRP
289
A
MET
290
n
263
MET
290
A
GLN
291
n
264
GLN
291
A
ASP
292
n
265
ASP
292
A
VAL
293
n
266
VAL
293
A
LEU
294
n
267
LEU
294
A
LEU
295
n
268
LEU
295
A
PRO
296
n
269
PRO
296
A
GLN
297
n
270
GLN
297
A
GLU
298
n
271
GLU
298
A
THR
299
n
272
THR
299
A
ALA
300
n
273
ALA
300
A
GLU
301
n
274
GLU
301
A
ILE
302
n
275
ILE
302
A
HIS
303
n
276
HIS
303
A
LEU
304
n
277
LEU
304
A
HIS
305
n
278
HIS
305
A
SER
306
n
279
SER
306
A
GLY
307
n
280
LEU
307
A
n
281
308
A
n
282
309
A
n
283
310
A
n
284
311
A
n
285
312
A
n
286
313
A
n
287
314
A
n
288
315
A
n
289
316
A
n
290
317
A
n
291
318
A
n
292
319
A
n
293
320
A
n
294
321
A
author_and_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
GLY
41
A
N
GLY
14
A
O
SER
54
A
O
SER
27
A
N
TYR
53
A
N
TYR
26
A
O
ILE
66
A
O
ILE
39
A
N
VAL
69
A
N
VAL
42
A
O
PHE
116
A
O
PHE
89
A
O
ILE
119
A
O
ILE
92
A
N
LEU
107
A
N
LEU
80
A
N
GLY
78
A
N
GLY
51
A
O
VAL
86
A
O
VAL
59
A
N
GLN
127
A
N
GLN
100
A
O
ILE
175
A
O
ILE
148
A
N
LEU
174
A
N
LEU
147
A
O
LYS
183
A
O
LYS
156
A
N
LEU
164
A
N
LEU
137
A
O
ALA
191
A
O
ALA
164
1
A
CB
LEU
307
A
CB
LEU
280
1
Y
1
A
CG
LEU
307
A
CG
LEU
280
1
Y
1
A
CD1
LEU
307
A
CD1
LEU
280
1
Y
1
A
CD2
LEU
307
A
CD2
LEU
280
1
Y
1
A
MET
28
A
MET
1
1
Y
1
A
LYS
29
A
LYS
2
1
Y
1
A
GLU
30
A
GLU
3
1
Y
1
A
LYS
31
A
LYS
4
1
Y
1
A
GLU
32
A
GLU
5
1
Y
1
A
SER
308
A
SER
281
1
Y
1
A
PRO
309
A
PRO
282
1
Y
1
A
GLY
310
A
GLY
283
1
Y
1
A
PRO
311
A
PRO
284
1
Y
1
A
SER
312
A
SER
285
1
Y
1
A
LYS
313
A
LYS
286
1
Y
1
A
VAL
314
A
VAL
287
1
Y
1
A
ASP
315
A
ASP
288
1
Y
1
A
HIS
316
A
HIS
289
1
Y
1
A
HIS
317
A
HIS
290
1
Y
1
A
HIS
318
A
HIS
291
1
Y
1
A
HIS
319
A
HIS
292
1
Y
1
A
HIS
320
A
HIS
293
1
Y
1
A
HIS
321
A
HIS
294
1
Y
1
-3.15
0.50
120.30
117.15
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
166
166
166
N
1
-5.71
0.90
118.30
112.59
A
A
A
CB
CG
OD1
ASP
ASP
ASP
202
202
202
A
A
A
N
1
3.62
0.50
120.30
123.92
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
205
205
205
N
1
6.08
0.90
118.30
124.38
A
A
A
CB
CG
OD1
ASP
ASP
ASP
239
239
239
N
1
4.90
0.50
120.30
125.20
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
268
268
268
N
1
-6.22
0.50
120.30
114.08
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
268
268
268
N
1
A
LEU
34
79.79
155.65
1
A
GLU
35
-97.12
49.45
1
A
SER
59
-27.52
-65.19
1
A
SER
98
146.63
-176.47
1
A
ASP
167
-150.56
42.17
1
A
ASP
186
67.14
86.13
1
A
ASP
202
A
-144.33
17.31
1
A
ASP
292
71.41
38.32
1
A
HIS
305
49.77
93.65
1
A
SER
306
-102.51
-83.53
32.765
0.12
0.06
-0.00
0.12
-0.00
-0.18
0.925
0.899
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25700
0.22393
0.22563
2.40
50
877
16490
5.0
99.80
7.068
0.166
RANDOM
1
THROUGHOUT
FOURIER SYNTHESIS
0.301
0.232
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
2.40
50
0
2256
22
0
2234
0.023
0.021
2319
2.176
1.960
3150
6.378
5.000
274
35.269
23.136
118
17.800
15.000
381
22.784
15.000
21
0.148
0.200
334
0.010
0.021
1825
1.172
1.500
1368
2.179
2.000
2216
3.322
3.000
951
5.121
4.500
934
0.366
0.325
2.462
67
1188
20
98.90
2.40
85.13
3JY0
17429
2
2
1
99.7
data collection
HKL-2000
refinement
REFMAC
5.5.0066
data reduction
HKL-2000
data scaling
SCALEPACK
Discovery of 3H-benzo[4,5]thieno[3,2-d]pyrimidin-4-ones as Potent, Highly Selective and Orally Bioavailable Pim Kinases Inhibitors
1
N
N
2
N
N
A
ASP
72
A
ASP
45
HELX_P
A
ILE
74
A
ILE
47
5
1
3
A
MET
88
A
MET
61
HELX_P
A
SER
97
A
SER
70
1
2
10
A
LEU
129
A
LEU
102
HELX_P
A
GLY
137
A
GLY
110
1
3
9
A
GLN
140
A
GLN
113
HELX_P
A
CYS
161
A
CYS
134
1
4
22
A
LYS
169
A
LYS
142
HELX_P
A
GLU
171
A
GLU
144
5
5
3
A
THR
204
A
THR
177
HELX_P
A
SER
208
A
SER
181
5
6
5
A
PRO
209
A
PRO
182
HELX_P
A
HIS
216
A
HIS
189
1
7
8
A
HIS
219
A
HIS
192
HELX_P
A
GLY
238
A
GLY
211
1
8
20
A
HIS
244
A
HIS
217
HELX_P
A
GLY
251
A
GLY
224
1
9
8
A
SER
260
A
SER
233
HELX_P
A
LEU
271
A
LEU
244
1
10
12
A
ARG
274
A
ARG
247
HELX_P
A
ARG
278
A
ARG
251
5
11
5
A
THR
280
A
THR
253
HELX_P
A
ASN
286
A
ASN
259
1
12
7
A
HIS
287
A
HIS
260
HELX_P
A
GLN
291
A
GLN
264
5
13
5
A
LEU
295
A
LEU
268
HELX_P
A
LEU
304
A
LEU
277
1
14
10
TRANSFERASE
PIM-1, Alternative initiation, ATP-binding, Cell membrane, Cytoplasm, Kinase, Manganese, Membrane, Metal-binding, Nucleotide-binding, Nucleus, Phosphoprotein, Polymorphism, Proto-oncogene, Serine/threonine-protein kinase, Transferase
A
GLU
124
A
GLU
97
1
A
PRO
125
A
PRO
98
-1.16
PIM1_HUMAN
UNP
1
120
P11309
KEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLD
WFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFG
SGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIR
WCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
120
404
3JY0
29
313
P11309
A
1
2
286
1
initiating methionine
MET
28
3JY0
A
P11309
UNP
1
1
expression tag
VAL
314
3JY0
A
P11309
UNP
287
1
expression tag
ASP
315
3JY0
A
P11309
UNP
288
1
expression tag
HIS
316
3JY0
A
P11309
UNP
289
1
expression tag
HIS
317
3JY0
A
P11309
UNP
290
1
expression tag
HIS
318
3JY0
A
P11309
UNP
291
1
expression tag
HIS
319
3JY0
A
P11309
UNP
292
1
expression tag
HIS
320
3JY0
A
P11309
UNP
293
1
expression tag
HIS
321
3JY0
A
P11309
UNP
294
5
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
38
A
TYR
11
A
LEU
43
A
LEU
16
A
SER
51
A
SER
24
A
ARG
57
A
ARG
30
A
PRO
63
A
PRO
36
A
GLU
70
A
GLU
43
A
SER
115
A
SER
88
A
GLU
121
A
GLU
94
A
LEU
106
A
LEU
79
A
GLU
111
A
GLU
84
A
TRP
77
A
TRP
50
A
GLU
79
A
GLU
52
A
ARG
85
A
ARG
58
A
PRO
87
A
PRO
60
A
VAL
126
A
VAL
99
A
ASP
128
A
ASP
101
A
ILE
173
A
ILE
146
A
ASP
176
A
ASP
149
A
GLU
181
A
GLU
154
A
LEU
184
A
LEU
157
A
VAL
163
A
VAL
136
A
LEU
164
A
LEU
137
A
ALA
191
A
ALA
164
A
LEU
192
A
LEU
165
BINDING SITE FOR RESIDUE LYG A 1000
A
LYG
1000
Software
8
A
ALA
65
A
ALA
38
8
1_555
A
LYS
67
A
LYS
40
8
1_555
A
GLU
121
A
GLU
94
8
1_555
A
GLU
171
A
GLU
144
8
1_555
A
ASN
172
A
ASN
145
8
1_555
A
LEU
174
A
LEU
147
8
1_555
A
ILE
185
A
ILE
158
8
1_555
A
ASP
186
A
ASP
159
8
1_555
170
P 65