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Receptor
PDB id Resolution Class Description Source Keywords
6BHV 2.3 Å EC: 2.4.2.30 HUMAN PARP-1 BOUND TO NAD+ ANALOG BENZAMIDE ADENINE DINUCLEO HOMO SAPIENS PARP-1 ARTD1 POLY(ADP-RIBOSE) POLYMERASE NON-HYDROLYZABLEANALOG PARP ADP-RIBOSE TRANSFERASE
Ref.: NAD+ANALOG REVEALS PARP-1 SUBSTRATE-BLOCKING MECHAN ALLOSTERIC COMMUNICATION FROM CATALYTIC CENTER TO DNA-BINDING DOMAINS. NAT COMMUN V. 9 844 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DQV B:1101;
D:1101;
A:1101;
C:1101;
 Valid;
Valid;
Valid;
Valid;
 Atoms found MORE than expected: % Diff = 1.25;
Atoms found MORE than expected: % Diff = 1.182;
Atoms found MORE than expected: % Diff = 1.182;
none;
 Kd = 5.87 uM
662.437 C22 H28 N6 O14 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6BHV 2.3 Å EC: 2.4.2.30 HUMAN PARP-1 BOUND TO NAD+ ANALOG BENZAMIDE ADENINE DINUCLEO HOMO SAPIENS PARP-1 ARTD1 POLY(ADP-RIBOSE) POLYMERASE NON-HYDROLYZABLEANALOG PARP ADP-RIBOSE TRANSFERASE
Ref.: NAD+ANALOG REVEALS PARP-1 SUBSTRATE-BLOCKING MECHAN ALLOSTERIC COMMUNICATION FROM CATALYTIC CENTER TO DNA-BINDING DOMAINS. NAT COMMUN V. 9 844 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
50% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5XSU ic50 = 244 nM 8E3 C15 H13 F N4 O2 c1c(cc2c(c....
2 4R6E ic50 = 132 nM 3JD C19 H20 N4 O c1cc2cn(nc....
3 4ZZZ Kd = 0.087 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
4 5XSR ic50 = 17 nM 8EC C15 H13 F N4 O S c1c(cc2c(c....
5 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
6 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
7 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
8 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
9 5XST ic50 = 27 nM 8E6 C15 H13 F N4 O S c1c(cc2c(c....
10 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
11 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
12 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
13 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
14 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
15 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
16 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
17 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
18 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
19 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
20 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
21 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
22 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
23 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
24 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
25 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
26 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
27 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
28 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
29 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
30 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
31 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
32 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
33 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
34 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
35 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
36 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DQV; Similar ligands found: 287
No: Ligand ECFP6 Tc MDL keys Tc
1 DQV 1 1
2 A2D 0.681319 0.985915
3 APR 0.649485 0.958333
4 AR6 0.649485 0.958333
5 BA3 0.648936 0.985915
6 AP5 0.642105 0.985915
7 B4P 0.642105 0.985915
8 M33 0.628866 0.945205
9 ADP 0.625 0.958333
10 ATP 0.622449 0.958333
11 HEJ 0.622449 0.958333
12 AT4 0.618557 0.92
13 AN2 0.618557 0.945205
14 AQP 0.616162 0.958333
15 5FA 0.616162 0.958333
16 CA0 0.612245 0.958904
17 3OD 0.611111 0.958904
18 AD9 0.61 0.932432
19 SAP 0.61 0.907895
20 AGS 0.61 0.907895
21 OOB 0.609524 0.972222
22 ACP 0.606061 0.932432
23 OAD 0.592593 0.958904
24 5AL 0.592233 0.945205
25 CNA 0.591667 0.972603
26 A1R 0.588785 0.896104
27 A22 0.584906 0.972222
28 PRX 0.584158 0.881579
29 00A 0.583333 0.921053
30 ACQ 0.582524 0.932432
31 ANP 0.582524 0.932432
32 NAX 0.581197 0.910256
33 DND 0.581197 0.972603
34 NXX 0.581197 0.972603
35 SRP 0.580952 0.92
36 ADX 0.58 0.8625
37 A 0.578947 0.930556
38 AMP 0.578947 0.930556
39 9X8 0.577982 0.907895
40 3UK 0.577982 0.958904
41 ABM 0.57732 0.905405
42 50T 0.574257 0.918919
43 A3R 0.574074 0.896104
44 B5V 0.572727 0.945946
45 ATF 0.571429 0.92
46 9SN 0.571429 0.909091
47 DLL 0.568807 0.972222
48 B5M 0.566372 0.933333
49 6YZ 0.566038 0.932432
50 8QN 0.564815 0.945205
51 DZD 0.564516 0.922078
52 PAJ 0.559633 0.897436
53 4AD 0.559633 0.933333
54 ADQ 0.559633 0.958904
55 WAQ 0.558559 0.896104
56 PR8 0.558559 0.8625
57 AHX 0.554545 0.909091
58 TXA 0.553571 0.945946
59 TAT 0.552381 0.92
60 T99 0.552381 0.92
61 AP2 0.55 0.92
62 A12 0.55 0.92
63 48N 0.546219 0.909091
64 AMO 0.545455 0.945946
65 NAD 0.544 0.972222
66 6V0 0.541667 0.934211
67 NAI 0.541667 0.946667
68 SRA 0.540816 0.881579
69 BIS 0.539823 0.896104
70 1ZZ 0.539823 0.851852
71 FA5 0.53913 0.945946
72 B5Y 0.53913 0.933333
73 APC 0.538462 0.92
74 OMR 0.53719 0.864198
75 TXE 0.53719 0.946667
76 25L 0.535088 0.972222
77 AU1 0.533981 0.932432
78 ADV 0.533333 0.92
79 RBY 0.533333 0.92
80 LAD 0.530973 0.873418
81 4UV 0.529915 0.933333
82 TAD 0.529412 0.897436
83 TXD 0.528926 0.946667
84 DAL AMP 0.527273 0.918919
85 ME8 0.526316 0.851852
86 PTJ 0.526316 0.884615
87 FYA 0.526316 0.918919
88 NB8 0.526316 0.909091
89 YAP 0.525862 0.933333
90 TYM 0.52459 0.945946
91 SON 0.524272 0.92
92 A3D 0.523438 0.958904
93 GAP 0.523364 0.906667
94 5SV 0.522523 0.8375
95 25A 0.522523 0.958333
96 9ZA 0.522523 0.896104
97 9ZD 0.522523 0.896104
98 AFH 0.521008 0.897436
99 ADP PO3 0.518868 0.930556
100 EAD 0.514925 0.910256
101 G3A 0.512605 0.934211
102 XAH 0.508475 0.851852
103 G5P 0.508333 0.934211
104 4UU 0.508333 0.933333
105 AP0 0.508065 0.909091
106 GTA 0.504132 0.898734
107 UP5 0.504065 0.959459
108 MAP 0.5 0.907895
109 P1H 0.5 0.8875
110 ALF ADP 0.5 0.858974
111 F2R 0.5 0.853659
112 LAQ 0.5 0.851852
113 80F 0.5 0.876543
114 ADP ALF 0.5 0.858974
115 M24 0.5 0.886076
116 NAE 0.496241 0.933333
117 COD 0.496124 0.823529
118 GA7 0.495868 0.92
119 ADP VO4 0.495495 0.918919
120 VO4 ADP 0.495495 0.918919
121 NAQ 0.492537 0.909091
122 4UW 0.491935 0.897436
123 A2R 0.491071 0.945205
124 PAP 0.490741 0.944444
125 ZID 0.488889 0.958904
126 LMS 0.485149 0.817073
127 139 0.484375 0.910256
128 ADJ 0.484375 0.864198
129 T5A 0.484375 0.876543
130 4TC 0.484127 0.934211
131 YLP 0.483871 0.831325
132 MYR AMP 0.483051 0.829268
133 2A5 0.481481 0.881579
134 AYB 0.48062 0.821429
135 A4P 0.480315 0.855422
136 TYR AMP 0.479339 0.907895
137 A A 0.478632 0.931507
138 NJP 0.476923 0.959459
139 IOT 0.476562 0.821429
140 AOC 0.475728 0.810811
141 ATP A A A 0.475 0.944444
142 9K8 0.474576 0.744444
143 53H 0.473684 0.790698
144 9JJ 0.473684 0.898734
145 FNK 0.472973 0.816092
146 YLA 0.472868 0.831325
147 YLB 0.472441 0.831325
148 UPA 0.472441 0.946667
149 YLC 0.472441 0.851852
150 ARG AMP 0.471545 0.819277
151 ADP BMA 0.470085 0.932432
152 BT5 0.469697 0.821429
153 AMP DBH 0.467213 0.906667
154 ATR 0.463636 0.930556
155 ITT 0.462963 0.90411
156 7D4 0.462963 0.868421
157 A3P 0.462264 0.930556
158 0WD 0.462121 0.934211
159 AMP NAD 0.462121 0.945205
160 FB0 0.461538 0.795455
161 NDC 0.461538 0.909091
162 NPW 0.461538 0.898734
163 TSB 0.46087 0.831325
164 A5A 0.460177 0.819277
165 G5A 0.459459 0.790698
166 5AS 0.457944 0.770115
167 NDE 0.457746 0.945946
168 LEU LMS 0.457627 0.764045
169 SSA 0.45614 0.811765
170 FDA 0.455172 0.845238
171 5CD 0.453608 0.794521
172 A4D 0.453608 0.808219
173 LSS 0.452991 0.772727
174 7D3 0.45283 0.868421
175 XYA 0.452632 0.833333
176 ADN 0.452632 0.833333
177 RAB 0.452632 0.833333
178 AHZ 0.452381 0.829268
179 VMS 0.452174 0.8
180 54H 0.452174 0.8
181 52H 0.452174 0.790698
182 NAJ PZO 0.451852 0.884615
183 PPS 0.451327 0.839506
184 JB6 0.45 0.896104
185 F0P 0.449612 0.7625
186 NVA LMS 0.449153 0.764045
187 LPA AMP 0.448819 0.829268
188 P5F 0.448718 0.835294
189 7MD 0.448 0.875
190 AV2 0.447368 0.88
191 HFD 0.446429 0.907895
192 NA7 0.445378 0.92
193 YLY 0.445255 0.821429
194 5N5 0.443299 0.808219
195 F2N 0.443038 0.825581
196 AF3 ADP 3PG 0.44186 0.85
197 NSS 0.440678 0.811765
198 BTX 0.440298 0.831325
199 XNP 0.440298 0.886076
200 EP4 0.44 0.74359
201 8PZ 0.439024 0.833333
202 NAJ PYZ 0.438849 0.841463
203 6AD 0.438596 0.873418
204 3DH 0.436893 0.763158
205 AR6 AR6 0.436508 0.931507
206 SFD 0.436242 0.763441
207 NZQ 0.43609 0.922078
208 5CA 0.435897 0.811765
209 8X1 0.435897 0.764045
210 NAP 0.435714 0.958904
211 N0B 0.435714 0.853659
212 DTA 0.435644 0.8
213 M2T 0.435644 0.725
214 62F 0.434211 0.875
215 3AM 0.432692 0.890411
216 6FA 0.432432 0.876543
217 5X8 0.432432 0.776316
218 AVV 0.432203 0.884615
219 FA9 0.43125 0.876543
220 WSA 0.430769 0.821429
221 P5A 0.429752 0.755556
222 NHD 0.42963 0.945205
223 DSZ 0.428571 0.811765
224 NDP 0.428571 0.934211
225 7MC 0.427481 0.853659
226 7D5 0.427184 0.842105
227 FAS 0.426667 0.8875
228 FAD 0.426667 0.8875
229 ARU 0.425 0.82716
230 6RE 0.424528 0.728395
231 YSA 0.424 0.811765
232 1DG 0.422535 0.934211
233 DG1 0.422535 0.934211
234 ODP 0.422222 0.922078
235 A2P 0.422018 0.916667
236 4YB 0.421875 0.793103
237 NA0 0.41958 0.945946
238 GSU 0.418033 0.790698
239 KAA 0.418033 0.764045
240 MTA 0.417476 0.763158
241 3AT 0.417391 0.931507
242 DCA 0.417266 0.813953
243 ETB 0.417266 0.823529
244 J7C 0.416667 0.7375
245 TXP 0.414815 0.934211
246 NFD 0.413043 0.921053
247 FAY 0.412903 0.898734
248 A5D 0.412281 0.8
249 COA 0.411348 0.813953
250 0T1 0.411348 0.813953
251 RFL 0.410256 0.855422
252 U A 0.410072 0.921053
253 N01 0.410072 0.945205
254 A6D 0.409836 0.73494
255 CMX 0.409722 0.813953
256 649 0.409091 0.775281
257 4TA 0.408759 0.841463
258 G A A A 0.408759 0.884615
259 SAH 0.408696 0.75641
260 DSH 0.407407 0.716049
261 NEC 0.407407 0.76
262 SFG 0.40708 0.763158
263 SMM 0.40678 0.697674
264 S7M 0.40678 0.702381
265 7C5 0.40625 0.831169
266 8Q2 0.406015 0.804598
267 SAM 0.405172 0.702381
268 DTP 0.405172 0.868421
269 V3L 0.405172 0.931507
270 A3N 0.40367 0.776316
271 IMO 0.40367 0.890411
272 TAP 0.402778 0.896104
273 COS 0.402778 0.795455
274 30N 0.402778 0.744681
275 CAO 0.402778 0.786517
276 AMX 0.402778 0.823529
277 ZAS 0.401869 0.75641
278 A3S 0.401786 0.824324
279 EEM 0.401709 0.702381
280 BYC 0.401316 0.816092
281 S4M 0.4 0.659091
282 SA8 0.4 0.719512
283 SCO 0.4 0.813953
284 GGZ 0.4 0.814815
285 AMZ 0.4 0.90411
286 GJV 0.4 0.719512
287 IVC 0.4 0.804598
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6BHV; Ligand: DQV; Similar sites found with APoc: 63
This union binding pocket(no: 1) in the query (biounit: 6bhv.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3UYW TAU 1.40187
2 4GK9 MAN BMA MAN MAN MAN 1.47601
3 3QPB URA 1.84502
4 5JH2 A2P 1.84502
5 3KVY URA 2.21402
6 5EWK P34 2.5
7 5W75 SUC 2.58303
8 1RYD GLC 2.95203
9 3R75 PYR 2.95203
10 2BTM PGA 2.95203
11 4EIL FOL 2.95203
12 2BHW XAT 3.01724
13 3SBZ MLI 3.1746
14 2XOM GAL GAL GAL 3.28947
15 1OJZ NAD 3.32103
16 4YC0 5OF 3.34728
17 4DDY DN6 3.42205
18 4Z9D NAD 3.42857
19 4ZH7 FUC GAL NAG GAL FUC 3.49908
20 1OG1 TAD 3.53982
21 1DTP APU 3.68421
22 1TOX NAD 3.69004
23 4LOC BTN 3.69004
24 4WMY 3S6 3.69004
25 5OCG 9R5 3.7037
26 1GZF NIR 3.79147
27 1GZF NAD 3.79147
28 1GZF ADP 3.79147
29 6FA4 D1W 4.04624
30 4RF7 ARG 4.05904
31 1QKQ MAN 4.05904
32 1QH9 LAC 4.31034
33 4H03 NAD 4.42804
34 4MPO AMP 4.57516
35 4YJK URA 4.7619
36 3Q9O NAD 4.79705
37 5H04 NAI 4.79705
38 1SBR VIB 5
39 3ITA AIC 5.16605
40 5IFK HPA 5.53506
41 3ESS 18N 5.65217
42 5DYO FLU 5.66038
43 1G51 AMP 5.90406
44 5I60 67W 5.96206
45 2A5F NAD 6.27306
46 2A9K NAD 6.41711
47 2YPI PGA 6.47773
48 4XZ3 ACP 6.52174
49 2WN6 NDP 8.11808
50 5KJW 53C 8.11808
51 2G30 ALA ALA PHE 8.13953
52 3B82 NAD 8.85609
53 2VDF OCT 9.22509
54 2F6U CIT 9.9631
55 2W5P CL8 10.0671
56 5ZJ5 NAI 10.4938
57 1T0S BML 12.7907
58 1XK9 P34 13.0233
59 5YSI NCA 13.1579
60 4FK7 P34 14.7601
61 4FXQ G9L 14.7601
62 4XSH NAI 15.5251
63 1DTL BEP 18.6335
Pocket No.: 2; Query (leader) PDB : 6BHV; Ligand: DQV; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 6bhv.bio4) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU None
2 2Q1A 2KT 5.53506
3 5YJS SAL 6.27306
4 2FKA BEF 6.97674
5 3IX9 MTX 7.36842
6 2CYB TYR 21.0332
Pocket No.: 3; Query (leader) PDB : 6BHV; Ligand: DQV; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 6bhv.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4CSD MFU 2.21402
2 4OJP MAL 5.53506
3 5N0J FAD 9.9631
Pocket No.: 4; Query (leader) PDB : 6BHV; Ligand: DQV; Similar sites found with APoc: 9
This union binding pocket(no: 4) in the query (biounit: 6bhv.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 5OC1 FAD 5.90406
2 1GPE FAD 6.64207
3 5KMS NAD 7.01107
4 1RJW ETF 7.38007
5 3LQV ADE 7.82609
6 6FU4 HSM 8.11808
7 4UUG PXG 8.85609
8 4CE5 PDG 8.85609
9 1IYE PGU 10.7011
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