0.024390
0.000000
0.003298
0.000000
0.011161
0.000000
0.000000
0.000000
0.024257
0.00000
0.00000
0.00000
Allerston, C.K.
Djordjevic, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
97.70
90.00
41.000
89.600
41.600
C17 H19 N7 O5 S3
497.572
(S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid
(2S)-2-[[3-(2,1,3-benzothiadiazol-4-ylsulfonylamino)thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
N
1
N
C
N
2
N
N
N
3
N
O
N
4
S
C
N
5
N
C
N
6
N
C
N
7
N
N
N
8
N
C
N
9
N
C
N
10
N
O
N
11
N
O
N
12
N
O
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
C
Y
17
N
C
Y
18
N
N
Y
19
N
N
N
20
N
N
Y
21
N
S
Y
22
N
S
N
23
N
C
Y
24
N
C
Y
25
N
C
Y
26
N
C
Y
27
N
C
Y
28
N
C
N
29
N
S
N
30
N
N
N
31
N
N
N
32
N
O
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
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
N
N
53
S
C
N
54
N
C
N
55
N
O
N
56
N
C
N
57
N
O
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
C
N
71
N
C
N
72
N
N
N
73
N
C
N
74
N
N
N
75
N
N
N
76
N
O
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
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
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
N
N
93
S
C
N
94
N
C
N
95
N
O
N
96
N
C
N
97
N
C
N
98
N
O
N
99
N
N
N
100
N
O
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
H
N
109
N
N
N
110
S
C
N
111
N
C
N
112
N
O
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
N
N
126
R
C
N
127
N
C
N
128
N
O
N
129
N
C
N
130
N
S
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
H
N
138
N
H
N
139
N
N
N
140
S
C
N
141
N
C
N
142
N
O
N
143
N
C
N
144
N
C
N
145
N
C
N
146
N
O
N
147
N
N
N
148
N
O
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
H
N
159
N
N
N
160
S
C
N
161
N
C
N
162
N
O
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
N
168
N
O
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
N
N
179
N
C
N
180
N
C
N
181
N
O
N
182
N
O
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
C
N
189
N
O
N
190
N
C
N
191
N
O
N
192
N
C
N
193
N
O
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
N
N
N
203
S
C
N
204
N
C
N
205
N
O
N
206
N
C
Y
207
N
C
Y
208
N
N
Y
209
N
C
Y
210
N
C
Y
211
N
N
N
212
N
O
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
O
N
224
N
H
N
225
N
H
N
226
N
N
N
227
S
C
N
228
N
C
N
229
N
O
N
230
S
C
N
231
N
C
N
232
N
C
N
233
N
C
N
234
N
O
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
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
N
253
N
C
N
254
N
C
N
255
N
C
N
256
N
O
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
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
N
N
279
N
O
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
N
N
296
S
C
N
297
N
C
N
298
N
O
N
299
N
C
N
300
N
C
N
301
N
S
N
302
N
C
N
303
N
O
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
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
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
C
Y
325
N
C
N
326
N
O
N
327
N
H
N
328
N
H
N
329
N
H
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
H
N
338
N
N
N
339
S
C
N
340
N
C
N
341
N
O
N
342
N
C
N
343
N
C
N
344
N
C
N
345
N
O
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
H
N
355
N
N
N
356
S
C
N
357
N
C
N
358
N
O
N
359
N
C
N
360
N
O
N
361
N
O
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
N
N
370
S
C
N
371
N
C
N
372
N
O
N
373
R
C
N
374
N
O
N
375
N
C
N
376
N
O
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
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
N
Y
395
N
C
Y
396
N
C
Y
397
N
C
Y
398
N
C
Y
399
N
C
N
400
N
O
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
N
N
414
S
C
N
415
N
C
N
416
N
O
N
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
C
Y
422
N
C
Y
423
N
C
N
424
N
O
N
425
N
O
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
N
N
438
S
C
N
439
N
C
N
440
N
O
N
441
N
C
N
442
N
C
N
443
N
C
N
444
N
O
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
1
N
sing
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
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
sing
N
20
N
doub
N
21
N
sing
N
22
N
doub
N
23
N
doub
N
24
N
doub
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
doub
N
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
sing
N
34
N
sing
Y
35
N
sing
N
36
N
sing
Y
37
N
doub
Y
38
N
sing
Y
39
N
doub
Y
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
Y
44
N
sing
N
45
N
sing
Y
46
N
doub
N
47
N
sing
Y
48
N
sing
Y
49
N
sing
N
50
N
sing
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
doub
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
doub
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
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
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
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
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
sing
N
127
N
sing
N
128
N
sing
N
129
N
doub
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
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
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
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
doub
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
doub
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
doub
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
N
200
N
sing
N
201
N
doub
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
Y
206
N
sing
Y
207
N
doub
Y
208
N
doub
N
209
N
sing
Y
210
N
sing
N
211
N
sing
Y
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
doub
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
sing
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
doub
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
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
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
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
doub
N
291
N
sing
N
292
N
sing
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
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
doub
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
Y
314
N
doub
Y
315
N
sing
Y
316
N
sing
N
317
N
sing
Y
318
N
doub
N
319
N
sing
Y
320
N
doub
N
321
N
sing
Y
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
doub
N
333
N
sing
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
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
doub
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
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
doub
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
Y
383
N
doub
Y
384
N
sing
Y
385
N
sing
N
386
N
sing
Y
387
N
doub
Y
388
N
sing
Y
389
N
sing
N
390
N
sing
Y
391
N
sing
Y
392
N
doub
N
393
N
sing
Y
394
N
doub
N
395
N
sing
Y
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
doub
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
sing
N
414
N
sing
Y
415
N
doub
N
416
N
sing
Y
417
N
doub
N
418
N
sing
Y
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
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
doub
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
US
J.Med.Chem.
JMCMAR
0151
0022-2623
53
2215
2226
10.1021/jm901755g
20151671
Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction.
2010
10.2210/pdb3i97/pdb
pdb_00003i97
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
OSMIC MIRRORS
IMAGE PLATE
2008-05-01
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU
17917.291
Neuropilin-1
domain B1, F5/8 type C 1
2
man
polymer
497.572
(S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid
2
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
8
nat
water
Vascular endothelial cell growth factor 165 receptor
no
no
GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET
KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT
GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET
KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT
A,B
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
human
sample
NP1-B1, NRP, NRP1, VEGF165R
9606
Homo sapiens
562
Escherichia coli
Rosetta
1
2.15
42.85
6
100 mM MES (pH 6.0), 10% PEG 8K and 200 mM Zn(AcO, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
293.15
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ncs_dom_lim
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2010-03-02
1
1
2011-07-13
1
2
2023-09-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ncs_dom_lim.beg_auth_comp_id
_struct_ncs_dom_lim.beg_label_asym_id
_struct_ncs_dom_lim.beg_label_comp_id
_struct_ncs_dom_lim.beg_label_seq_id
_struct_ncs_dom_lim.end_auth_comp_id
_struct_ncs_dom_lim.end_label_asym_id
_struct_ncs_dom_lim.end_label_comp_id
_struct_ncs_dom_lim.end_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2009-07-10
REL
REL
8DR
(S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid
GOL
GLYCEROL
HOH
water
1KEX
PDB ENTRY 1KEX
PDB
experimental model
8DR
156
2
8DR
8DR
156
A
GOL
157
3
GOL
GOL
157
A
8DR
156
2
8DR
8DR
156
B
HOH
158
4
HOH
HOH
158
A
HOH
159
4
HOH
HOH
159
A
HOH
160
4
HOH
HOH
160
A
HOH
161
4
HOH
HOH
161
A
HOH
162
4
HOH
HOH
162
A
HOH
163
4
HOH
HOH
163
A
HOH
164
4
HOH
HOH
164
A
HOH
157
4
HOH
HOH
157
B
n
1
-2
A
n
2
-1
A
n
3
0
A
n
4
1
A
LYS
2
n
5
LYS
2
A
CYS
3
n
6
CYS
3
A
MET
4
n
7
MET
4
A
GLU
5
n
8
GLU
5
A
ALA
6
n
9
ALA
6
A
LEU
7
n
10
LEU
7
A
GLY
8
n
11
GLY
8
A
MET
9
n
12
MET
9
A
GLU
10
n
13
GLU
10
A
SER
11
n
14
SER
11
A
GLY
12
n
15
GLY
12
A
GLU
13
n
16
GLU
13
A
ILE
14
n
17
ILE
14
A
HIS
15
n
18
HIS
15
A
SER
16
n
19
SER
16
A
ASP
17
n
20
ASP
17
A
GLN
18
n
21
GLN
18
A
ILE
19
n
22
ILE
19
A
THR
20
n
23
THR
20
A
ALA
21
n
24
ALA
21
A
SER
22
n
25
SER
22
A
SER
23
n
26
SER
23
A
GLN
24
n
27
GLN
24
A
TYR
25
n
28
TYR
25
A
SER
26
n
29
SER
26
A
THR
27
n
30
THR
27
A
ASN
28
n
31
ASN
28
A
TRP
29
n
32
TRP
29
A
SER
30
n
33
SER
30
A
ALA
31
n
34
ALA
31
A
GLU
32
n
35
GLU
32
A
ARG
33
n
36
ARG
33
A
SER
34
n
37
SER
34
A
ARG
35
n
38
ARG
35
A
LEU
36
n
39
LEU
36
A
ASN
37
n
40
ASN
37
A
TYR
38
n
41
TYR
38
A
PRO
39
n
42
PRO
39
A
GLU
40
n
43
GLU
40
A
ASN
41
n
44
ASN
41
A
GLY
42
n
45
GLY
42
A
TRP
43
n
46
TRP
43
A
THR
44
n
47
THR
44
A
PRO
45
n
48
PRO
45
A
GLY
46
n
49
GLY
46
A
GLU
47
n
50
GLU
47
A
ASP
48
n
51
ASP
48
A
SER
49
n
52
SER
49
A
TYR
50
n
53
TYR
50
A
ARG
51
n
54
ARG
51
A
GLU
52
n
55
GLU
52
A
TRP
53
n
56
TRP
53
A
ILE
54
n
57
ILE
54
A
GLN
55
n
58
GLN
55
A
VAL
56
n
59
VAL
56
A
ASP
57
n
60
ASP
57
A
LEU
58
n
61
LEU
58
A
GLY
59
n
62
GLY
59
A
LEU
60
n
63
LEU
60
A
LEU
61
n
64
LEU
61
A
ARG
62
n
65
ARG
62
A
PHE
63
n
66
PHE
63
A
VAL
64
n
67
VAL
64
A
THR
65
n
68
THR
65
A
ALA
66
n
69
ALA
66
A
VAL
67
n
70
VAL
67
A
GLY
68
n
71
GLY
68
A
THR
69
n
72
THR
69
A
GLN
70
n
73
GLN
70
A
GLY
71
n
74
GLY
71
A
ALA
72
n
75
ALA
72
A
ILE
73
n
76
ILE
73
A
SER
74
n
77
SER
74
A
LYS
75
n
78
LYS
75
A
GLU
76
n
79
GLU
76
A
THR
77
n
80
THR
77
A
LYS
78
n
81
LYS
78
A
LYS
79
n
82
LYS
79
A
LYS
80
n
83
LYS
80
A
TYR
81
n
84
TYR
81
A
TYR
82
n
85
TYR
82
A
VAL
83
n
86
VAL
83
A
LYS
84
n
87
LYS
84
A
THR
85
n
88
THR
85
A
TYR
86
n
89
TYR
86
A
LYS
87
n
90
LYS
87
A
ILE
88
n
91
ILE
88
A
ASP
89
n
92
ASP
89
A
VAL
90
n
93
VAL
90
A
SER
91
n
94
SER
91
A
SER
92
n
95
SER
92
A
ASN
93
n
96
ASN
93
A
GLY
94
n
97
GLY
94
A
GLU
95
n
98
GLU
95
A
ASP
96
n
99
ASP
96
A
TRP
97
n
100
TRP
97
A
ILE
98
n
101
ILE
98
A
THR
99
n
102
THR
99
A
ILE
100
n
103
ILE
100
A
LYS
101
n
104
LYS
101
A
GLU
102
n
105
GLU
102
A
GLY
103
n
106
GLY
103
A
ASN
104
n
107
ASN
104
A
LYS
105
n
108
LYS
105
A
PRO
106
n
109
PRO
106
A
VAL
107
n
110
VAL
107
A
LEU
108
n
111
LEU
108
A
PHE
109
n
112
PHE
109
A
GLN
110
n
113
GLN
110
A
GLY
111
n
114
GLY
111
A
ASN
112
n
115
ASN
112
A
THR
113
n
116
THR
113
A
ASN
114
n
117
ASN
114
A
PRO
115
n
118
PRO
115
A
THR
116
n
119
THR
116
A
ASP
117
n
120
ASP
117
A
VAL
118
n
121
VAL
118
A
VAL
119
n
122
VAL
119
A
VAL
120
n
123
VAL
120
A
ALA
121
n
124
ALA
121
A
VAL
122
n
125
VAL
122
A
PHE
123
n
126
PHE
123
A
PRO
124
n
127
PRO
124
A
LYS
125
n
128
LYS
125
A
PRO
126
n
129
PRO
126
A
LEU
127
n
130
LEU
127
A
ILE
128
n
131
ILE
128
A
THR
129
n
132
THR
129
A
ARG
130
n
133
ARG
130
A
PHE
131
n
134
PHE
131
A
VAL
132
n
135
VAL
132
A
ARG
133
n
136
ARG
133
A
ILE
134
n
137
ILE
134
A
LYS
135
n
138
LYS
135
A
PRO
136
n
139
PRO
136
A
ALA
137
n
140
ALA
137
A
THR
138
n
141
THR
138
A
TRP
139
n
142
TRP
139
A
GLU
140
n
143
GLU
140
A
THR
141
n
144
THR
141
A
GLY
142
n
145
GLY
142
A
ILE
143
n
146
ILE
143
A
SER
144
n
147
SER
144
A
MET
145
n
148
MET
145
A
ARG
146
n
149
ARG
146
A
PHE
147
n
150
PHE
147
A
GLU
148
n
151
GLU
148
A
VAL
149
n
152
VAL
149
A
TYR
150
n
153
TYR
150
A
GLY
151
n
154
GLY
151
A
CYS
152
n
155
CYS
152
A
LYS
153
n
156
LYS
153
A
ILE
154
n
157
ILE
154
A
THR
155
n
158
THR
155
A
n
1
-2
B
n
2
-1
B
n
3
0
B
n
4
1
B
LYS
2
n
5
LYS
2
B
CYS
3
n
6
CYS
3
B
MET
4
n
7
MET
4
B
GLU
5
n
8
GLU
5
B
ALA
6
n
9
ALA
6
B
LEU
7
n
10
LEU
7
B
GLY
8
n
11
GLY
8
B
MET
9
n
12
MET
9
B
GLU
10
n
13
GLU
10
B
SER
11
n
14
SER
11
B
GLY
12
n
15
GLY
12
B
GLU
13
n
16
GLU
13
B
ILE
14
n
17
ILE
14
B
HIS
15
n
18
HIS
15
B
SER
16
n
19
SER
16
B
ASP
17
n
20
ASP
17
B
GLN
18
n
21
GLN
18
B
ILE
19
n
22
ILE
19
B
THR
20
n
23
THR
20
B
ALA
21
n
24
ALA
21
B
SER
22
n
25
SER
22
B
SER
23
n
26
SER
23
B
GLN
24
n
27
GLN
24
B
TYR
25
n
28
TYR
25
B
SER
26
n
29
SER
26
B
THR
27
n
30
THR
27
B
ASN
28
n
31
ASN
28
B
TRP
29
n
32
TRP
29
B
SER
30
n
33
SER
30
B
ALA
31
n
34
ALA
31
B
GLU
32
n
35
GLU
32
B
ARG
33
n
36
ARG
33
B
SER
34
n
37
SER
34
B
ARG
35
n
38
ARG
35
B
LEU
36
n
39
LEU
36
B
ASN
37
n
40
ASN
37
B
TYR
38
n
41
TYR
38
B
PRO
39
n
42
PRO
39
B
GLU
40
n
43
GLU
40
B
ASN
41
n
44
ASN
41
B
GLY
42
n
45
GLY
42
B
TRP
43
n
46
TRP
43
B
THR
44
n
47
THR
44
B
PRO
45
n
48
PRO
45
B
GLY
46
n
49
GLY
46
B
GLU
47
n
50
GLU
47
B
ASP
48
n
51
ASP
48
B
SER
49
n
52
SER
49
B
TYR
50
n
53
TYR
50
B
ARG
51
n
54
ARG
51
B
GLU
52
n
55
GLU
52
B
TRP
53
n
56
TRP
53
B
ILE
54
n
57
ILE
54
B
GLN
55
n
58
GLN
55
B
VAL
56
n
59
VAL
56
B
ASP
57
n
60
ASP
57
B
LEU
58
n
61
LEU
58
B
GLY
59
n
62
GLY
59
B
LEU
60
n
63
LEU
60
B
LEU
61
n
64
LEU
61
B
ARG
62
n
65
ARG
62
B
PHE
63
n
66
PHE
63
B
VAL
64
n
67
VAL
64
B
THR
65
n
68
THR
65
B
ALA
66
n
69
ALA
66
B
VAL
67
n
70
VAL
67
B
GLY
68
n
71
GLY
68
B
THR
69
n
72
THR
69
B
GLN
70
n
73
GLN
70
B
GLY
71
n
74
GLY
71
B
ALA
72
n
75
ALA
72
B
ILE
73
n
76
ILE
73
B
SER
74
n
77
SER
74
B
LYS
75
n
78
LYS
75
B
GLU
76
n
79
GLU
76
B
THR
77
n
80
THR
77
B
LYS
78
n
81
LYS
78
B
LYS
79
n
82
LYS
79
B
LYS
80
n
83
LYS
80
B
TYR
81
n
84
TYR
81
B
TYR
82
n
85
TYR
82
B
VAL
83
n
86
VAL
83
B
LYS
84
n
87
LYS
84
B
THR
85
n
88
THR
85
B
TYR
86
n
89
TYR
86
B
LYS
87
n
90
LYS
87
B
ILE
88
n
91
ILE
88
B
ASP
89
n
92
ASP
89
B
VAL
90
n
93
VAL
90
B
SER
91
n
94
SER
91
B
SER
92
n
95
SER
92
B
ASN
93
n
96
ASN
93
B
GLY
94
n
97
GLY
94
B
GLU
95
n
98
GLU
95
B
ASP
96
n
99
ASP
96
B
TRP
97
n
100
TRP
97
B
ILE
98
n
101
ILE
98
B
THR
99
n
102
THR
99
B
ILE
100
n
103
ILE
100
B
LYS
101
n
104
LYS
101
B
GLU
102
n
105
GLU
102
B
GLY
103
n
106
GLY
103
B
ASN
104
n
107
ASN
104
B
LYS
105
n
108
LYS
105
B
PRO
106
n
109
PRO
106
B
VAL
107
n
110
VAL
107
B
LEU
108
n
111
LEU
108
B
PHE
109
n
112
PHE
109
B
GLN
110
n
113
GLN
110
B
GLY
111
n
114
GLY
111
B
ASN
112
n
115
ASN
112
B
THR
113
n
116
THR
113
B
ASN
114
n
117
ASN
114
B
PRO
115
n
118
PRO
115
B
THR
116
n
119
THR
116
B
ASP
117
n
120
ASP
117
B
VAL
118
n
121
VAL
118
B
VAL
119
n
122
VAL
119
B
VAL
120
n
123
VAL
120
B
ALA
121
n
124
ALA
121
B
VAL
122
n
125
VAL
122
B
PHE
123
n
126
PHE
123
B
PRO
124
n
127
PRO
124
B
LYS
125
n
128
LYS
125
B
PRO
126
n
129
PRO
126
B
LEU
127
n
130
LEU
127
B
ILE
128
n
131
ILE
128
B
THR
129
n
132
THR
129
B
ARG
130
n
133
ARG
130
B
PHE
131
n
134
PHE
131
B
VAL
132
n
135
VAL
132
B
ARG
133
n
136
ARG
133
B
ILE
134
n
137
ILE
134
B
LYS
135
n
138
LYS
135
B
PRO
136
n
139
PRO
136
B
ALA
137
n
140
ALA
137
B
THR
138
n
141
THR
138
B
TRP
139
n
142
TRP
139
B
GLU
140
n
143
GLU
140
B
THR
141
n
144
THR
141
B
GLY
142
n
145
GLY
142
B
ILE
143
n
146
ILE
143
B
SER
144
n
147
SER
144
B
MET
145
n
148
MET
145
B
ARG
146
n
149
ARG
146
B
PHE
147
n
150
PHE
147
B
GLU
148
n
151
GLU
148
B
VAL
149
n
152
VAL
149
B
TYR
150
n
153
TYR
150
B
GLY
151
n
154
GLY
151
B
CYS
152
n
155
CYS
152
B
LYS
153
n
156
LYS
153
B
ILE
154
n
157
ILE
154
B
THR
155
n
158
THR
155
B
author_and_software_defined_assembly
PISA
1
monomeric
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
1
A
GLY
-2
A
GLY
1
1
Y
1
A
HIS
-1
A
HIS
2
1
Y
1
A
MET
0
A
MET
3
1
Y
1
A
PHE
1
A
PHE
4
1
Y
1
B
GLY
-2
B
GLY
1
1
Y
1
B
HIS
-1
B
HIS
2
1
Y
1
B
MET
0
B
MET
3
1
Y
1
B
PHE
1
B
PHE
4
1
Y
1
9.31
1.50
119.30
128.61
A
A
A
C
N
CA
LYS
PRO
PRO
105
106
106
Y
1
A
CYS
3
-151.50
77.95
1
A
MET
4
-150.70
47.64
1
A
SER
23
-170.08
-176.82
1
A
SER
26
179.96
168.18
1
A
TRP
29
-141.56
42.27
1
A
ASN
41
59.59
-149.91
1
A
ARG
51
-66.99
8.37
1
A
LEU
60
179.69
167.05
1
A
GLU
95
-120.23
-53.46
1
A
PRO
106
-30.45
118.39
1
A
ARG
130
-143.47
-36.17
1
A
THR
141
71.05
-56.43
1
B
SER
23
-171.15
-177.82
1
B
SER
26
178.28
170.57
1
B
TRP
29
-143.81
40.64
1
B
ASN
41
58.13
-151.70
1
B
LYS
78
76.88
-0.75
1
B
ASN
93
-146.15
21.74
1
B
ARG
130
-137.12
-38.57
1
B
THR
141
72.22
-56.65
16.96
0.43000
0.00000
-0.14000
-0.82000
0.00000
0.35000
0.924
0.829
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.282
0.216
0.219
2.90
30.33
278
5573
4.800
87.8
30.153
0.280
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.585
0.80
0.80
1.20
PDB ENTRY 1KEX
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.90
30.33
8
2533
70
0
2455
0.012
0.022
2588
1.416
1.970
3513
4.432
5.000
306
30.513
24.182
110
14.543
15.000
438
17.784
15.000
14
0.082
0.200
376
0.003
0.020
1954
0.247
0.300
1156
0.332
0.500
1784
0.179
0.500
148
0.320
0.300
40
0.201
0.500
2
0.405
2.000
1569
0.660
3.000
2510
0.355
2.000
1195
0.561
3.000
1003
1
A
1
316
X-RAY DIFFRACTION
tight positional
0.04
0.05
1
A
2
300
X-RAY DIFFRACTION
tight positional
0.06
0.05
1
A
3
321
X-RAY DIFFRACTION
tight positional
0.04
0.05
1
A
1
316
X-RAY DIFFRACTION
tight thermal
0.07
0.50
1
A
2
300
X-RAY DIFFRACTION
tight thermal
0.19
0.50
1
A
3
321
X-RAY DIFFRACTION
tight thermal
0.16
0.50
0.341
0.297
2.97
15
396
20
83.20
2.900
30.33
3I97
5852
0.079
1
8.5000
2.400
88
0.191
2.9
3.0
4.0
2.3
85.4
data collection
CrystalClear
phasing
PHASER
refinement
REFMAC
5.2.0019
data reduction
d*TREK
data scaling
d*TREK
B1 domain of human Neuropilin-1 bound with small molecule EG00229
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
4
N
N
4
N
N
A
HIS
15
A
HIS
18
HELX_P
A
ASP
17
A
ASP
20
5
1
3
A
SER
26
A
SER
29
HELX_P
A
SER
34
A
SER
37
5
2
9
B
HIS
15
B
HIS
18
HELX_P
B
ASP
17
B
ASP
20
5
3
3
B
SER
26
B
SER
29
HELX_P
B
SER
34
B
SER
37
5
4
9
disulf
2.019
A
CYS
3
A
SG
CYS
6
1_555
A
CYS
152
A
SG
CYS
155
1_555
disulf
2.043
B
CYS
3
B
SG
CYS
6
1_555
B
CYS
152
B
SG
CYS
155
1_555
SIGNALING PROTEIN
Neuropilin-1, Drug, VEGF, Angiogenesis, Neuropilin, Alternative splicing, Cell membrane, Developmental protein, Differentiation, Disulfide bond, Glycoprotein, Heparan sulfate, Membrane, Neurogenesis, Phosphoprotein, Polymorphism, Proteoglycan, Receptor, Secreted, Transmembrane, MEMBRANE PROTEIN, SIGNALING PROTEIN
A
B
A
B
A
B
A
GLU
5
A
GLU
8
A
THR
44
A
THR
47
1
B
GLU
5
B
GLU
8
B
THR
44
B
THR
47
1
A
ILE
54
A
ILE
57
A
SER
91
A
SER
94
1
B
ILE
54
B
ILE
57
B
SER
91
B
SER
94
1
A
GLY
111
A
GLY
114
A
TYR
150
A
TYR
153
1
B
GLY
111
B
GLY
114
B
TYR
150
B
TYR
153
1
NRP1_HUMAN
UNP
1
273
O14786
FKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKK
YYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT
273
427
3I97
1
155
O14786
A
1
4
158
273
427
3I97
1
155
O14786
B
1
4
158
1
expression tag
GLY
-2
3I97
A
O14786
UNP
1
1
expression tag
HIS
-1
3I97
A
O14786
UNP
2
1
expression tag
MET
0
3I97
A
O14786
UNP
3
2
expression tag
GLY
-2
3I97
B
O14786
UNP
1
2
expression tag
HIS
-1
3I97
B
O14786
UNP
2
2
expression tag
MET
0
3I97
B
O14786
UNP
3
BINDING SITE FOR RESIDUE 8DR A 156
A
8DR
156
Software
12
BINDING SITE FOR RESIDUE GOL A 157
A
GOL
157
Software
3
BINDING SITE FOR RESIDUE 8DR B 156
B
8DR
156
Software
12
A
TYR
25
A
TYR
28
12
1_555
A
SER
26
A
SER
29
12
1_555
A
THR
44
A
THR
47
12
1_555
A
ASP
48
A
ASP
51
12
1_555
A
SER
74
A
SER
77
12
1_555
A
GLU
76
A
GLU
79
12
1_555
A
THR
77
A
THR
80
12
1_555
A
TYR
81
A
TYR
84
12
1_555
A
GLY
142
A
GLY
145
12
1_555
A
ILE
143
A
ILE
146
12
1_555
B
MET
4
B
MET
7
12
1_454
B
VAL
120
B
VAL
123
12
1_454
A
SER
26
A
SER
29
3
1_555
A
THR
27
A
THR
30
3
1_555
A
ASN
28
A
ASN
31
3
1_555
B
TYR
25
B
TYR
28
12
1_555
B
SER
26
B
SER
29
12
1_555
B
ASN
28
B
ASN
31
12
1_555
B
TRP
29
B
TRP
32
12
1_555
B
THR
44
B
THR
47
12
1_555
B
ASP
48
B
ASP
51
12
1_555
B
SER
74
B
SER
77
12
1_555
B
GLU
76
B
GLU
79
12
1_555
B
THR
77
B
THR
80
12
1_555
B
TYR
81
B
TYR
84
12
1_555
B
GLY
142
B
GLY
145
12
1_555
B
ILE
143
B
ILE
146
12
1_555
4
P 1 21 1