Receptor
PDB id Resolution Class Description Source Keywords
3NIF 2.4 Å NON-ENZYME: OTHER THE CLOSED HEADPIECE OF INTEGRIN IIB 3 AND ITS COMPLEX WITH SPECIFIC ANTAGONIST THAT DOES NOT INDUCE OPENING HOMO SAPIENS INTEGRIN HEADPIECE ALPHAIIB BETA3 CELL ADHESION-BLOOD CLCOMPLEX
Ref.: CLOSED HEADPIECE OF INTEGRIN {ALPHA}IIB{BETA}3 AND COMPLEX WITH AN {ALPHA}IIB{BETA}3-SPECIFIC ANTAGONI DOES NOT INDUCE OPENING. BLOOD V. 116 5050 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:2004;
A:2005;
A:2006;
A:2007;
B:2002;
B:2003;
C:2004;
C:2005;
C:2006;
C:2007;
D:2002;
D:2003;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
GOL A:456;
A:457;
A:458;
A:459;
A:460;
A:461;
B:472;
D:472;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG B:2001;
D:2001;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
NAG B:3099;
D:3099;
Part of Protein;
Part of Protein;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG K:1;
I:1;
Part of Protein;
Part of Protein;
none;
none;
submit data
408.404 n/a O=C(N...
NAG NAG MAN J:1;
Part of Protein;
none;
submit data
n/a n/a
NAG NAG MAN MAN G:1;
Part of Protein;
none;
submit data
n/a n/a
NIF A:455;
C:455;
Valid;
Valid;
none;
none;
submit data
265.335 C11 H15 N5 O S CCC1=...
SO4 A:462;
A:463;
A:464;
A:465;
A:466;
B:473;
C:456;
C:457;
C:458;
C:459;
C:460;
C:461;
D:473;
D:474;
D:475;
H:222;
L:215;
L:216;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ZE2 2.35 Å NON-ENZYME: OTHER INTEGRIN ALPHAIIB BETA3 HEADPIECE AND RGD PEPTIDE COMPLEX HOMO SAPIENS CELL ADHESION-IMMUNE SYSTEM-PEPTIDE COMPLEX CELL ADHESIN-IMSYSTEM-PEPTIDE COMPLEX CELL ADHESION
Ref.: COMPLETE INTEGRIN HEADPIECE OPENING IN EIGHT STEPS. J.CELL BIOL. V. 201 1053 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3NIF - NIF C11 H15 N5 O S CCC1=NN2C(....
2 3ZDY - GLY ARG GLY ASP SER PRO n/a n/a
3 3ZE2 - GLY ARG GLY ASP SER PRO n/a n/a
4 2VDR - LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3NIF - NIF C11 H15 N5 O S CCC1=NN2C(....
2 3ZDY - GLY ARG GLY ASP SER PRO n/a n/a
3 3ZE2 - GLY ARG GLY ASP SER PRO n/a n/a
4 2VDR - LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL n/a n/a
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3GJF Kd = 46 nM SER LEU LEU MET TRP ILE THR GLN VAL n/a n/a
2 2ZPK - PRO ARG GLY TYR PRO GLY GLN VAL n/a n/a
3 3NIF - NIF C11 H15 N5 O S CCC1=NN2C(....
4 3ZDY - GLY ARG GLY ASP SER PRO n/a n/a
5 3ZE2 - GLY ARG GLY ASP SER PRO n/a n/a
6 2VDR - LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL n/a n/a
7 3WFD - AXO C2 H5 N O C/C=N/O
8 4XTR - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1W72 Kd = 14 nM GLU ALA ASP PRO THR GLY HIS SER TYR n/a n/a
10 6O24 - CIT C6 H8 O7 C(C(=O)O)C....
11 6ID4 Kd = 0.000000064 M ALA ILE PHE GLN SER SER MET THR LYS n/a n/a
12 5X2N - ALA C3 H7 N O2 C[C@@H](C(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NIF; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NIF 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: NIF; Similar ligands found: 499
No: Ligand Similarity coefficient
1 1V4 0.9615
2 1V3 0.9606
3 40N 0.9470
4 6QT 0.9461
5 F40 0.9407
6 P4L 0.9392
7 7L4 0.9385
8 0UL 0.9381
9 DFL 0.9375
10 20D 0.9372
11 LIG 0.9344
12 PIQ 0.9340
13 NKI 0.9336
14 3GX 0.9323
15 DDC 0.9306
16 A73 0.9282
17 25F 0.9279
18 6JO 0.9273
19 RGK 0.9272
20 1V1 0.9265
21 5NN 0.9264
22 SZ5 0.9262
23 1FE 0.9260
24 CUE 0.9259
25 3F4 0.9254
26 FCW 0.9251
27 0DF 0.9247
28 7EH 0.9247
29 2GQ 0.9246
30 AJG 0.9242
31 HH6 0.9241
32 YZ9 0.9239
33 A05 0.9238
34 II4 0.9236
35 WLH 0.9233
36 7EL 0.9227
37 3SU 0.9224
38 57D 0.9219
39 272 0.9210
40 AJ1 0.9209
41 SNJ 0.9202
42 NPS 0.9199
43 3WL 0.9196
44 62D 0.9188
45 9CE 0.9184
46 Q0K 0.9178
47 Q8D 0.9175
48 121 0.9173
49 Q8G 0.9169
50 RSV 0.9169
51 HRD 0.9168
52 UN3 0.9167
53 FSE 0.9165
54 6DQ 0.9165
55 1Q4 0.9163
56 M3W 0.9155
57 E9L 0.9146
58 1HP 0.9146
59 YE7 0.9141
60 5NR 0.9136
61 AGI 0.9131
62 6JM 0.9130
63 H2W 0.9130
64 O9Z 0.9129
65 MMJ 0.9128
66 C4E 0.9127
67 DXK 0.9125
68 O9T 0.9122
69 W8L 0.9112
70 CDJ 0.9112
71 NRA 0.9110
72 IDZ 0.9100
73 3JC 0.9099
74 801 0.9099
75 COL 0.9097
76 7G2 0.9094
77 124 0.9088
78 O9Q 0.9086
79 A6W 0.9086
80 K4T 0.9082
81 6B5 0.9082
82 0OK 0.9079
83 LU2 0.9074
84 VT3 0.9069
85 122 0.9065
86 RF2 0.9063
87 H4B 0.9061
88 OTA 0.9054
89 FT6 0.9053
90 CX4 0.9052
91 39R 0.9046
92 4QX 0.9046
93 DX2 0.9045
94 LC1 0.9041
95 AD6 0.9038
96 3DE 0.9037
97 5DE 0.9033
98 KP2 0.9033
99 A9B 0.9032
100 1R5 0.9032
101 7LU 0.9031
102 2D2 0.9030
103 GEN 0.9027
104 LI7 0.9022
105 7FU 0.9022
106 BBP 0.9021
107 120 0.9021
108 6XC 0.9020
109 D64 0.9020
110 27F 0.9017
111 0NJ 0.9013
112 NAR 0.9008
113 5F8 0.9008
114 DFV 0.9006
115 0SX 0.9005
116 3D8 0.9005
117 7KE 0.9004
118 5FL 0.9001
119 A63 0.9000
120 EZL 0.8997
121 90M 0.8996
122 IQW 0.8994
123 4NR 0.8994
124 LR2 0.8991
125 SJR 0.8990
126 5E5 0.8990
127 1V8 0.8989
128 4R0 0.8989
129 5S9 0.8986
130 08C 0.8985
131 Q4G 0.8985
132 NYJ 0.8985
133 ZSP 0.8984
134 AJD 0.8984
135 6BK 0.8981
136 90G 0.8974
137 NPX 0.8973
138 78Y 0.8971
139 AO 0.8970
140 OPA 0.8968
141 KMP 0.8966
142 FYR 0.8964
143 5TT 0.8963
144 109 0.8961
145 4AU 0.8960
146 4CN 0.8959
147 5B2 0.8959
148 1UZ 0.8955
149 9JT 0.8953
150 P7V 0.8949
151 AVX 0.8948
152 Y3L 0.8947
153 ZAR 0.8947
154 5E2 0.8946
155 2QU 0.8945
156 5WT 0.8940
157 4UM 0.8939
158 BVS 0.8938
159 LWS 0.8937
160 5KN 0.8936
161 6FX 0.8936
162 4Z1 0.8934
163 20N 0.8934
164 AX1 0.8927
165 H2B 0.8926
166 0MB 0.8920
167 CX6 0.8919
168 PRL 0.8917
169 91F 0.8915
170 BMZ 0.8915
171 QUE 0.8914
172 HBI 0.8914
173 AVA 0.8913
174 IK1 0.8913
175 1DR 0.8913
176 H0V 0.8912
177 AP6 0.8908
178 L2K 0.8905
179 3WK 0.8904
180 IQQ 0.8904
181 JCZ 0.8903
182 D26 0.8902
183 UAY 0.8900
184 CR4 0.8900
185 5P3 0.8894
186 5WW 0.8893
187 HHB 0.8893
188 15Q 0.8888
189 47V 0.8888
190 HA6 0.8887
191 LZ7 0.8886
192 TRP 0.8886
193 833 0.8882
194 4L2 0.8882
195 DBE 0.8879
196 U14 0.8878
197 DX7 0.8878
198 JSX 0.8878
199 2WU 0.8874
200 5ZM 0.8873
201 VBC 0.8872
202 28A 0.8871
203 BHS 0.8869
204 LL1 0.8867
205 AH6 0.8864
206 BRY 0.8863
207 L5D 0.8862
208 GB4 0.8861
209 2QV 0.8861
210 7M2 0.8861
211 NVS 0.8860
212 3C5 0.8859
213 H75 0.8856
214 39Z 0.8855
215 108 0.8854
216 HMZ 0.8853
217 BIO 0.8852
218 AMR 0.8851
219 2JX 0.8849
220 BZM 0.8848
221 2GE 0.8846
222 397 0.8846
223 27M 0.8846
224 18E 0.8845
225 AXX 0.8845
226 I0G 0.8843
227 LUM 0.8840
228 5TO 0.8838
229 BGU 0.8838
230 D25 0.8837
231 5VU 0.8837
232 51Y 0.8834
233 SAK 0.8834
234 3MI 0.8832
235 CHQ 0.8831
236 60L 0.8831
237 CWE 0.8831
238 97K 0.8829
239 EST 0.8829
240 338 0.8828
241 FY8 0.8828
242 RVE 0.8827
243 92O 0.8825
244 3WO 0.8824
245 3WN 0.8824
246 G2V 0.8823
247 5TZ 0.8820
248 SO7 0.8819
249 BBY 0.8818
250 M78 0.8817
251 205 0.8817
252 S60 0.8817
253 A8D 0.8816
254 MKN 0.8815
255 8CC 0.8815
256 S1D 0.8814
257 OLU 0.8814
258 01I 0.8814
259 1EL 0.8814
260 5E1 0.8813
261 S98 0.8812
262 697 0.8810
263 5V7 0.8810
264 4FF 0.8810
265 H35 0.8809
266 LZ4 0.8809
267 1AJ 0.8808
268 4HG 0.8807
269 KU1 0.8806
270 2J1 0.8806
271 0SY 0.8805
272 K7H 0.8804
273 SNB 0.8803
274 4GU 0.8803
275 4DE 0.8803
276 WDW 0.8801
277 AQN 0.8801
278 19E 0.8801
279 6P3 0.8801
280 363 0.8797
281 EQU 0.8796
282 52F 0.8795
283 NEO 0.8795
284 GJG 0.8794
285 5C1 0.8793
286 IOP 0.8790
287 23M 0.8790
288 AUV 0.8790
289 QS4 0.8790
290 4AB 0.8788
291 8M5 0.8786
292 M4N 0.8786
293 JTF 0.8784
294 6C5 0.8783
295 QIV 0.8782
296 MT6 0.8781
297 M83 0.8781
298 XIF XYP 0.8779
299 IQZ 0.8779
300 ZRK 0.8777
301 EES 0.8775
302 SU9 0.8774
303 E6Q 0.8774
304 TCR 0.8772
305 WS7 0.8771
306 196 0.8771
307 BJ4 0.8766
308 JMG 0.8766
309 VM1 0.8764
310 KLS 0.8764
311 6FB 0.8761
312 B7H 0.8761
313 EY2 0.8758
314 4UE 0.8756
315 22T 0.8754
316 X2M 0.8753
317 Z3R 0.8750
318 517 0.8745
319 N5B 0.8744
320 GUS 0.8744
321 609 0.8742
322 MYU 0.8742
323 MBT 0.8741
324 6VW 0.8740
325 A64 0.8735
326 QUG 0.8734
327 XZ1 0.8734
328 6DH 0.8733
329 B4L 0.8732
330 5F5 0.8732
331 6C8 0.8731
332 HMX 0.8729
333 U12 0.8727
334 ZRL 0.8726
335 49P 0.8726
336 TEF 0.8724
337 4B8 0.8722
338 SGW 0.8722
339 4ZF 0.8721
340 JRO 0.8720
341 802 0.8720
342 MYC 0.8716
343 MRI 0.8716
344 4I8 0.8715
345 RKV 0.8714
346 NK5 0.8714
347 YE6 0.8713
348 A5H 0.8712
349 XYP XIF 0.8711
350 RCV 0.8710
351 0FR 0.8710
352 V2Z 0.8709
353 878 0.8708
354 657 0.8706
355 2P3 0.8705
356 FHV 0.8704
357 XYP XDN 0.8704
358 8SK 0.8703
359 A98 0.8702
360 C0W 0.8702
361 DX8 0.8702
362 SDN 0.8701
363 BHF 0.8701
364 68B 0.8701
365 SVG 0.8700
366 NAL 0.8698
367 ET0 0.8697
368 U4J 0.8697
369 6ZE 0.8696
370 XDN XYP 0.8696
371 IQ5 0.8694
372 J38 0.8694
373 1EB 0.8692
374 4QY 0.8691
375 1UT 0.8691
376 NU3 0.8690
377 MXD 0.8689
378 F18 0.8688
379 761 0.8688
380 2PK 0.8688
381 1XS 0.8684
382 KLV 0.8682
383 KWB 0.8682
384 HCC 0.8681
385 E3U 0.8681
386 IDD 0.8680
387 KWV 0.8679
388 RHN 0.8678
389 B61 0.8678
390 5OR 0.8677
391 EAA 0.8676
392 CC6 0.8674
393 U55 0.8673
394 MUK 0.8673
395 1V0 0.8671
396 T21 0.8670
397 DN8 0.8668
398 FNT 0.8667
399 HUL 0.8667
400 IXM 0.8667
401 8HH 0.8667
402 9BF 0.8666
403 NFZ 0.8666
404 BIT 0.8665
405 1KX 0.8665
406 UV4 0.8661
407 5ER 0.8661
408 GNV 0.8660
409 MUR 0.8660
410 0H5 0.8656
411 EAT 0.8655
412 27K 0.8655
413 LR8 0.8654
414 TPM 0.8653
415 S62 0.8652
416 T34 0.8652
417 KF5 0.8651
418 NG6 0.8649
419 041 0.8648
420 4Z9 0.8648
421 HNT 0.8646
422 O53 0.8646
423 T61 0.8646
424 DQH 0.8646
425 ESZ 0.8644
426 HRM 0.8643
427 B21 0.8643
428 Q5M 0.8641
429 16G 0.8638
430 6FG 0.8638
431 3Y7 0.8638
432 7ZL 0.8637
433 4G2 0.8637
434 1FL 0.8637
435 F36 0.8635
436 ZEA 0.8633
437 MJW 0.8633
438 CG 0.8633
439 JFS 0.8632
440 WV7 0.8631
441 17M 0.8630
442 0RA 0.8629
443 OUA 0.8626
444 SSY 0.8626
445 9X3 0.8625
446 J1K 0.8624
447 HWB 0.8623
448 0LO 0.8622
449 78P 0.8622
450 1OT 0.8617
451 KSF 0.8616
452 S0J 0.8615
453 2OX 0.8615
454 7AP 0.8612
455 3C3 0.8610
456 0K7 0.8610
457 OUG 0.8608
458 BU7 0.8607
459 P4T 0.8607
460 JHY 0.8606
461 6NZ 0.8605
462 LEL 0.8602
463 JF8 0.8601
464 X2L 0.8600
465 DTQ 0.8597
466 X48 0.8592
467 NDD 0.8592
468 ADL 0.8591
469 0LA 0.8589
470 2PW 0.8588
471 TMG 0.8585
472 IS2 0.8585
473 CLI 0.8583
474 XCG 0.8582
475 2UD 0.8580
476 1UR 0.8580
477 6SD 0.8579
478 0ON 0.8578
479 AZN 0.8574
480 JVD 0.8572
481 ECS 0.8570
482 PMM 0.8570
483 Q7U 0.8567
484 3VQ 0.8565
485 3VX 0.8563
486 M3F 0.8561
487 UN9 0.8559
488 2LW 0.8558
489 4YF 0.8555
490 JF5 0.8554
491 N1E 0.8554
492 U7E 0.8550
493 AOM 0.8550
494 36K 0.8547
495 L02 0.8544
496 ZZA 0.8541
497 69W 0.8534
498 8NB 0.8532
499 ZEZ 0.8529
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ZE2; Ligand: GLY ARG GLY ASP SER PRO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3ze2.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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