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 LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
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
6NRF 2 Å EC: 2.4.2.30 CRYSTAL STRUCTURE OF HUMAN PARP-1 ART DOMAIN BOUND TO INHIBI HOMO SAPIENS PARP-1 POLY(ADP-RIBOSE) POLYMERASE PARP INHIBITOR PARP1 TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DESIGN AND SYNTHESIS OF POLY(ADP-RIBOSE) POLYMERASE INHIBITORS: IMPACT OF ADENOSINE POCKET-BINDING MOTI APPENDAGE TO THE 3-OXO-2,3-DIHYDROBENZOFURAN-7-CARB ON POTENCY AND SELECTIVITY. J.MED.CHEM. V. 62 5330 2019
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
2 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
3 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
4 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
5 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
6 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
2 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
3 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
4 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
5 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
6 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
50% Homology Family (43)
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 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
32 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
33 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
34 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
35 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
36 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
37 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
38 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
39 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
40 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
41 6I8T - H7Z C21 H29 N3 O2 C[C@@H]1c2....
42 6I8M - H7W C21 H29 N3 O2 C[C@H]1c2c....
43 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DQV; Similar ligands found: 308
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 B4P 0.642105 0.985915
7 AP5 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 AN2 0.618557 0.945205
13 AT4 0.618557 0.92
14 5FA 0.616162 0.958333
15 AQP 0.616162 0.958333
16 CA0 0.612245 0.958904
17 3OD 0.611111 0.958904
18 AD9 0.61 0.932432
19 AGS 0.61 0.907895
20 SAP 0.61 0.907895
21 OOB 0.609524 0.972222
22 ACP 0.606061 0.932432
23 KG4 0.606061 0.958904
24 8LQ 0.6 0.92
25 OAD 0.592593 0.958904
26 5AL 0.592233 0.945205
27 CNA 0.591667 0.972603
28 HQG 0.590476 0.945205
29 A1R 0.588785 0.896104
30 A22 0.584906 0.972222
31 PRX 0.584158 0.881579
32 00A 0.583333 0.921053
33 ACQ 0.582524 0.932432
34 ANP 0.582524 0.932432
35 NXX 0.581197 0.972603
36 DND 0.581197 0.972603
37 NAX 0.581197 0.910256
38 SRP 0.580952 0.92
39 8LH 0.580952 0.92
40 ADX 0.58 0.8625
41 A 0.578947 0.930556
42 AMP 0.578947 0.930556
43 3UK 0.577982 0.958904
44 9X8 0.577982 0.907895
45 45A 0.57732 0.905405
46 ABM 0.57732 0.905405
47 8LE 0.576923 0.907895
48 50T 0.574257 0.918919
49 A3R 0.574074 0.896104
50 B5V 0.572727 0.945946
51 ATF 0.571429 0.92
52 9SN 0.571429 0.909091
53 DLL 0.568807 0.972222
54 B5M 0.566372 0.933333
55 6YZ 0.566038 0.932432
56 8QN 0.564815 0.945205
57 DZD 0.564516 0.922078
58 4AD 0.559633 0.933333
59 ADQ 0.559633 0.958904
60 PAJ 0.559633 0.897436
61 PR8 0.558559 0.8625
62 WAQ 0.558559 0.896104
63 AHX 0.554545 0.909091
64 TXA 0.553571 0.945946
65 TAT 0.552381 0.92
66 T99 0.552381 0.92
67 OZV 0.550459 0.958333
68 A12 0.55 0.92
69 AP2 0.55 0.92
70 48N 0.546219 0.909091
71 AMO 0.545455 0.945946
72 NAD 0.544 0.972222
73 6V0 0.541667 0.934211
74 NAI 0.541667 0.946667
75 SRA 0.540816 0.881579
76 1ZZ 0.539823 0.851852
77 BIS 0.539823 0.896104
78 ADP MG 0.539216 0.930556
79 B5Y 0.53913 0.933333
80 FA5 0.53913 0.945946
81 APC 0.538462 0.92
82 TXE 0.53719 0.946667
83 OMR 0.53719 0.864198
84 25L 0.535088 0.972222
85 AU1 0.533981 0.932432
86 ADV 0.533333 0.92
87 RBY 0.533333 0.92
88 LAD 0.530973 0.873418
89 4UV 0.529915 0.933333
90 TAD 0.529412 0.897436
91 TXD 0.528926 0.946667
92 DAL AMP 0.527273 0.918919
93 NB8 0.526316 0.909091
94 ME8 0.526316 0.851852
95 PTJ 0.526316 0.884615
96 FYA 0.526316 0.918919
97 YAP 0.525862 0.933333
98 TYM 0.52459 0.945946
99 SON 0.524272 0.92
100 A3D 0.523438 0.958904
101 GAP 0.523364 0.906667
102 25A 0.522523 0.958333
103 5SV 0.522523 0.8375
104 9ZA 0.522523 0.896104
105 9ZD 0.522523 0.896104
106 AFH 0.521008 0.897436
107 APC MG 0.518868 0.905405
108 ATP MG 0.518868 0.930556
109 ADP PO3 0.518868 0.930556
110 EAD 0.514925 0.910256
111 G3A 0.512605 0.934211
112 XAH 0.508475 0.851852
113 4UU 0.508333 0.933333
114 G5P 0.508333 0.934211
115 AP0 0.508065 0.909091
116 GTA 0.504132 0.898734
117 UP5 0.504065 0.959459
118 M24 0.5 0.886076
119 P1H 0.5 0.8875
120 ADP ALF 0.5 0.858974
121 80F 0.5 0.876543
122 ALF ADP 0.5 0.858974
123 MAP 0.5 0.907895
124 F2R 0.5 0.853659
125 LAQ 0.5 0.851852
126 NAE 0.496241 0.933333
127 COD 0.496124 0.823529
128 GA7 0.495868 0.92
129 ADP VO4 0.495495 0.918919
130 VO4 ADP 0.495495 0.918919
131 NAQ 0.492537 0.909091
132 4UW 0.491935 0.897436
133 A2R 0.491071 0.945205
134 PAP 0.490741 0.944444
135 ZID 0.488889 0.958904
136 LMS 0.485149 0.817073
137 T5A 0.484375 0.876543
138 139 0.484375 0.910256
139 ADJ 0.484375 0.864198
140 4TC 0.484127 0.934211
141 YLP 0.483871 0.831325
142 MYR AMP 0.483051 0.829268
143 2A5 0.481481 0.881579
144 AYB 0.48062 0.821429
145 A4P 0.480315 0.855422
146 TYR AMP 0.479339 0.907895
147 A A 0.478632 0.931507
148 NJP 0.476923 0.959459
149 IOT 0.476562 0.821429
150 AOC 0.475728 0.810811
151 ATP A A A 0.475 0.944444
152 ATP A 0.475 0.944444
153 9K8 0.474576 0.744444
154 53H 0.473684 0.790698
155 9JJ 0.473684 0.898734
156 FNK 0.472973 0.816092
157 YLA 0.472868 0.831325
158 YLC 0.472441 0.851852
159 YLB 0.472441 0.831325
160 UPA 0.472441 0.946667
161 OZP 0.472 0.7625
162 ARG AMP 0.471545 0.819277
163 ADP BMA 0.470085 0.932432
164 BT5 0.469697 0.821429
165 AMP DBH 0.467213 0.906667
166 ATR 0.463636 0.930556
167 ITT 0.462963 0.90411
168 7D4 0.462963 0.868421
169 A3P 0.462264 0.930556
170 AMP NAD 0.462121 0.945205
171 0WD 0.462121 0.934211
172 NDC 0.461538 0.909091
173 FB0 0.461538 0.795455
174 NPW 0.461538 0.898734
175 TSB 0.46087 0.831325
176 A5A 0.460177 0.819277
177 G5A 0.459459 0.790698
178 5AS 0.457944 0.770115
179 NDE 0.457746 0.945946
180 LEU LMS 0.457627 0.764045
181 SSA 0.45614 0.811765
182 FDA 0.455172 0.845238
183 5CD 0.453608 0.794521
184 A4D 0.453608 0.808219
185 LSS 0.452991 0.772727
186 7D3 0.45283 0.868421
187 RAB 0.452632 0.833333
188 XYA 0.452632 0.833333
189 ADN 0.452632 0.833333
190 AHZ 0.452381 0.829268
191 VMS 0.452174 0.8
192 52H 0.452174 0.790698
193 54H 0.452174 0.8
194 NAJ PZO 0.451852 0.884615
195 PPS 0.451327 0.839506
196 JB6 0.45 0.896104
197 F0P 0.449612 0.7625
198 NVA LMS 0.449153 0.764045
199 LPA AMP 0.448819 0.829268
200 P5F 0.448718 0.835294
201 7MD 0.448 0.875
202 AV2 0.447368 0.88
203 JSQ 0.446429 0.907895
204 HFD 0.446429 0.907895
205 NA7 0.445378 0.92
206 YLY 0.445255 0.821429
207 5N5 0.443299 0.808219
208 F2N 0.443038 0.825581
209 AF3 ADP 3PG 0.44186 0.85
210 NSS 0.440678 0.811765
211 XNP 0.440298 0.886076
212 BTX 0.440298 0.831325
213 EP4 0.44 0.74359
214 8PZ 0.439024 0.833333
215 NAJ PYZ 0.438849 0.841463
216 6AD 0.438596 0.873418
217 KOY 0.4375 0.84
218 3DH 0.436893 0.763158
219 AR6 AR6 0.436508 0.931507
220 SFD 0.436242 0.763441
221 NZQ 0.43609 0.922078
222 8X1 0.435897 0.764045
223 5CA 0.435897 0.811765
224 N0B 0.435714 0.853659
225 NAP 0.435714 0.958904
226 DTA 0.435644 0.8
227 M2T 0.435644 0.725
228 B1U 0.435484 0.766667
229 62F 0.434211 0.875
230 3AM 0.432692 0.890411
231 5X8 0.432432 0.776316
232 6FA 0.432432 0.876543
233 H1Q 0.432432 0.891892
234 AVV 0.432203 0.884615
235 FA9 0.43125 0.876543
236 WSA 0.430769 0.821429
237 N37 0.430769 0.769231
238 P5A 0.429752 0.755556
239 NHD 0.42963 0.945205
240 NDP 0.428571 0.934211
241 DSZ 0.428571 0.811765
242 7MC 0.427481 0.853659
243 7D5 0.427184 0.842105
244 FAD 0.426667 0.8875
245 FAS 0.426667 0.8875
246 ARU 0.425 0.82716
247 6RE 0.424528 0.728395
248 YSA 0.424 0.811765
249 DG1 0.422535 0.934211
250 1DG 0.422535 0.934211
251 ODP 0.422222 0.922078
252 A2P 0.422018 0.916667
253 4YB 0.421875 0.793103
254 NA0 0.41958 0.945946
255 KAA 0.418033 0.764045
256 GSU 0.418033 0.790698
257 MTA 0.417476 0.763158
258 3AT 0.417391 0.931507
259 DCA 0.417266 0.813953
260 ETB 0.417266 0.823529
261 J7C 0.416667 0.7375
262 NO7 0.415254 0.894737
263 TXP 0.414815 0.934211
264 NFD 0.413043 0.921053
265 FAY 0.412903 0.898734
266 LQJ 0.412698 0.931507
267 A5D 0.412281 0.8
268 COA 0.411348 0.813953
269 0T1 0.411348 0.813953
270 RFL 0.410256 0.855422
271 N01 0.410072 0.945205
272 U A 0.410072 0.921053
273 A6D 0.409836 0.73494
274 CMX 0.409722 0.813953
275 649 0.409091 0.775281
276 G A A A 0.408759 0.884615
277 4TA 0.408759 0.841463
278 SAH 0.408696 0.75641
279 NEC 0.407407 0.76
280 DSH 0.407407 0.716049
281 SFG 0.40708 0.763158
282 S7M 0.40678 0.702381
283 SMM 0.40678 0.697674
284 J4G 0.406504 0.907895
285 7C5 0.40625 0.831169
286 8Q2 0.406015 0.804598
287 DTP 0.405172 0.868421
288 SAM 0.405172 0.702381
289 V3L 0.405172 0.931507
290 A3N 0.40367 0.776316
291 IMO 0.40367 0.890411
292 30N 0.402778 0.744681
293 CAO 0.402778 0.786517
294 TAP 0.402778 0.896104
295 COS 0.402778 0.795455
296 AMX 0.402778 0.823529
297 ZAS 0.401869 0.75641
298 A3S 0.401786 0.824324
299 EEM 0.401709 0.702381
300 BYC 0.401316 0.816092
301 S4M 0.4 0.659091
302 GJV 0.4 0.719512
303 IVC 0.4 0.804598
304 6MZ 0.4 0.891892
305 SA8 0.4 0.719512
306 AMZ 0.4 0.90411
307 GGZ 0.4 0.814815
308 SCO 0.4 0.813953
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6NRF; Ligand: KYV; 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: 6nrf.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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