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
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 (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 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 6NTU - GLC FRU n/a n/a
5 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
6 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
7 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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 6NTU - GLC FRU n/a n/a
5 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
6 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
7 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5XSU Kd = 180 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 Kd = 0.000000064 M 8EC C15 H13 F N4 O S c1c(cc2c(c....
5 6VKK - RPB C19 H18 F N3 O CNCc1ccc(c....
6 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
7 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
8 4HHY ic50 = 1.92 nM 15R C33 H30 F N5 O4 c1ccc2c(c1....
9 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
10 5XST ic50 = 27 nM 8E6 C15 H13 F N4 O S c1c(cc2c(c....
11 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
12 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
13 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
14 6XVW - O3H C19 H21 N5 O S c1ccc2c(c1....
15 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
16 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
17 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
18 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
19 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
20 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
21 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
22 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
23 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
24 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
25 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
26 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
27 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
28 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
29 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
30 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
31 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
32 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
33 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
34 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
35 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
36 6NTU - GLC FRU n/a n/a
37 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
38 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
39 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
40 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
41 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
42 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
43 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
44 6I8T - H7Z C21 H29 N3 O2 C[C@@H]1c2....
45 6I8M - H7W C21 H29 N3 O2 C[C@H]1c2c....
46 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DQV; Similar ligands found: 324
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 HEJ 0.622449 0.958333
11 ATP 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 AGS 0.61 0.907895
19 AD9 0.61 0.932432
20 OOB 0.609524 0.972222
21 ACP 0.606061 0.932432
22 KG4 0.606061 0.958904
23 8LQ 0.6 0.92
24 OAD 0.592593 0.958904
25 5AL 0.592233 0.945205
26 CNA 0.591667 0.972603
27 HQG 0.590476 0.945205
28 A1R 0.588785 0.896104
29 QA7 0.584906 0.907895
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 DND 0.581197 0.972603
36 NAX 0.581197 0.910256
37 8LH 0.580952 0.92
38 SRP 0.580952 0.92
39 ADX 0.58 0.8625
40 A 0.578947 0.930556
41 AMP 0.578947 0.930556
42 9X8 0.577982 0.907895
43 3UK 0.577982 0.958904
44 ABM 0.57732 0.905405
45 45A 0.57732 0.905405
46 8LE 0.576923 0.907895
47 50T 0.574257 0.918919
48 A3R 0.574074 0.896104
49 AMP MG 0.572917 0.916667
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 JNT 0.568807 0.932432
55 B5M 0.566372 0.933333
56 6YZ 0.566038 0.932432
57 8QN 0.564815 0.945205
58 DZD 0.564516 0.922078
59 ADQ 0.559633 0.958904
60 4AD 0.559633 0.933333
61 PAJ 0.559633 0.897436
62 PR8 0.558559 0.8625
63 WAQ 0.558559 0.896104
64 AHX 0.554545 0.909091
65 TXA 0.553571 0.945946
66 KMQ 0.552632 0.92
67 TAT 0.552381 0.92
68 T99 0.552381 0.92
69 OZV 0.550459 0.958333
70 A12 0.55 0.92
71 AP2 0.55 0.92
72 48N 0.546219 0.909091
73 AMO 0.545455 0.945946
74 NAD 0.544 0.972222
75 NAI 0.541667 0.946667
76 6V0 0.541667 0.934211
77 SRA 0.540816 0.881579
78 BIS 0.539823 0.896104
79 1ZZ 0.539823 0.851852
80 ADP MG 0.539216 0.930556
81 ADP BEF 0.539216 0.930556
82 B5Y 0.53913 0.933333
83 FA5 0.53913 0.945946
84 APC 0.538462 0.92
85 TXE 0.53719 0.946667
86 OMR 0.53719 0.864198
87 25L 0.535088 0.972222
88 AU1 0.533981 0.932432
89 RBY 0.533333 0.92
90 ADV 0.533333 0.92
91 L3W 0.532787 0.945946
92 V2G 0.53271 0.884615
93 LAD 0.530973 0.873418
94 4UV 0.529915 0.933333
95 TAD 0.529412 0.897436
96 TXD 0.528926 0.946667
97 BEF ADP 0.528302 0.905405
98 DAL AMP 0.527273 0.918919
99 PTJ 0.526316 0.884615
100 FYA 0.526316 0.918919
101 NB8 0.526316 0.909091
102 ME8 0.526316 0.851852
103 TYM 0.52459 0.945946
104 SON 0.524272 0.92
105 A3D 0.523438 0.958904
106 GAP 0.523364 0.906667
107 5SV 0.522523 0.8375
108 9ZA 0.522523 0.896104
109 25A 0.522523 0.958333
110 9ZD 0.522523 0.896104
111 AFH 0.521008 0.897436
112 ADP PO3 0.518868 0.930556
113 ATP MG 0.518868 0.930556
114 APC MG 0.518868 0.905405
115 EAD 0.514925 0.910256
116 G3A 0.512605 0.934211
117 XAH 0.508475 0.851852
118 4UU 0.508333 0.933333
119 G5P 0.508333 0.934211
120 AP0 0.508065 0.909091
121 NAD IBO 0.508065 0.958333
122 NAD TDB 0.508065 0.958333
123 GTA 0.504132 0.898734
124 UP5 0.504065 0.959459
125 MAP 0.5 0.907895
126 F2R 0.5 0.853659
127 ALF ADP 0.5 0.858974
128 VO4 ADP 0.5 0.906667
129 ANP MG 0.5 0.918919
130 P1H 0.5 0.8875
131 M24 0.5 0.886076
132 80F 0.5 0.876543
133 LAQ 0.5 0.851852
134 NAE 0.496241 0.933333
135 COD 0.496124 0.823529
136 GA7 0.495868 0.92
137 NAQ 0.492537 0.909091
138 4UW 0.491935 0.897436
139 A2R 0.491071 0.945205
140 PAP 0.490741 0.944444
141 ZID 0.488889 0.958904
142 LMS 0.485149 0.817073
143 ADJ 0.484375 0.864198
144 T5A 0.484375 0.876543
145 139 0.484375 0.910256
146 4TC 0.484127 0.934211
147 YLP 0.483871 0.831325
148 MYR AMP 0.483051 0.829268
149 2A5 0.481481 0.881579
150 AYB 0.48062 0.821429
151 A4P 0.480315 0.855422
152 NJP 0.476923 0.959459
153 IOT 0.476562 0.821429
154 AOC 0.475728 0.810811
155 ATP A A A 0.475 0.944444
156 ATP A 0.475 0.944444
157 9K8 0.474576 0.744444
158 53H 0.473684 0.790698
159 9JJ 0.473684 0.898734
160 FNK 0.472973 0.816092
161 YLA 0.472868 0.831325
162 YLC 0.472441 0.851852
163 YLB 0.472441 0.831325
164 UPA 0.472441 0.946667
165 OZP 0.472 0.7625
166 ARG AMP 0.471545 0.819277
167 ADP BMA 0.470085 0.932432
168 BT5 0.469697 0.821429
169 AMP DBH 0.467213 0.906667
170 ATR 0.463636 0.930556
171 D4F 0.463235 0.875
172 ITT 0.462963 0.90411
173 7D4 0.462963 0.868421
174 A3P 0.462264 0.930556
175 0WD 0.462121 0.934211
176 AMP NAD 0.462121 0.945205
177 NDC 0.461538 0.909091
178 FB0 0.461538 0.795455
179 NPW 0.461538 0.898734
180 TSB 0.46087 0.831325
181 A5A 0.460177 0.819277
182 G5A 0.459459 0.790698
183 5AS 0.457944 0.770115
184 NDE 0.457746 0.945946
185 LEU LMS 0.457627 0.741573
186 SSA 0.45614 0.811765
187 V47 0.45614 0.821918
188 FDA 0.455172 0.845238
189 R2V 0.453782 0.797619
190 A4D 0.453608 0.808219
191 5CD 0.453608 0.794521
192 ALF ADP 3PG 0.453125 0.85
193 LSS 0.452991 0.772727
194 7D3 0.45283 0.868421
195 RAB 0.452632 0.833333
196 ADN 0.452632 0.833333
197 XYA 0.452632 0.833333
198 AHZ 0.452381 0.829268
199 54H 0.452174 0.8
200 52H 0.452174 0.790698
201 VMS 0.452174 0.8
202 NAJ PZO 0.451852 0.884615
203 PPS 0.451327 0.839506
204 JB6 0.45 0.896104
205 F0P 0.449612 0.7625
206 NVA LMS 0.449153 0.764045
207 LPA AMP 0.448819 0.829268
208 P5F 0.448718 0.835294
209 7MD 0.448 0.875
210 AV2 0.447368 0.88
211 JSQ 0.446429 0.907895
212 HFD 0.446429 0.907895
213 38V 0.446043 0.898734
214 NA7 0.445378 0.92
215 YLY 0.445255 0.821429
216 5N5 0.443299 0.808219
217 F2N 0.443038 0.825581
218 AF3 ADP 3PG 0.44186 0.85
219 NSS 0.440678 0.811765
220 XNP 0.440298 0.886076
221 BTX 0.440298 0.831325
222 EP4 0.44 0.74359
223 8PZ 0.439024 0.833333
224 NAJ PYZ 0.438849 0.841463
225 6AD 0.438596 0.873418
226 KOY 0.4375 0.84
227 3DH 0.436893 0.763158
228 AR6 AR6 0.436508 0.931507
229 SFD 0.436242 0.763441
230 NZQ 0.43609 0.922078
231 8X1 0.435897 0.764045
232 5CA 0.435897 0.811765
233 NAP 0.435714 0.958904
234 N0B 0.435714 0.853659
235 M2T 0.435644 0.725
236 DTA 0.435644 0.8
237 B1U 0.435484 0.766667
238 62F 0.434211 0.875
239 3AM 0.432692 0.890411
240 6FA 0.432432 0.876543
241 H1Q 0.432432 0.891892
242 5X8 0.432432 0.776316
243 QXP 0.432203 0.797619
244 AVV 0.432203 0.884615
245 FA9 0.43125 0.876543
246 WSA 0.430769 0.821429
247 N37 0.430769 0.769231
248 P5A 0.429752 0.755556
249 NHD 0.42963 0.945205
250 NDP 0.428571 0.934211
251 DSZ 0.428571 0.811765
252 7MC 0.427481 0.853659
253 7D5 0.427184 0.842105
254 FAD 0.426667 0.8875
255 FAS 0.426667 0.8875
256 FAJ 0.425926 0.865854
257 ARU 0.425 0.82716
258 NAD CJ3 0.424837 0.845238
259 6RE 0.424528 0.728395
260 YSA 0.424 0.811765
261 DG1 0.422535 0.934211
262 1DG 0.422535 0.934211
263 ODP 0.422222 0.922078
264 A2P 0.422018 0.916667
265 4YB 0.421875 0.793103
266 QXG 0.421488 0.788235
267 NAD BBN 0.421053 0.876543
268 NA0 0.41958 0.945946
269 KAA 0.418033 0.764045
270 GSU 0.418033 0.790698
271 MTA 0.417476 0.763158
272 3AT 0.417391 0.931507
273 DCA 0.417266 0.813953
274 ETB 0.417266 0.823529
275 J7C 0.416667 0.7375
276 NO7 0.415254 0.894737
277 TXP 0.414815 0.934211
278 NFD 0.413043 0.921053
279 FAY 0.412903 0.898734
280 LQJ 0.412698 0.931507
281 A5D 0.412281 0.8
282 0T1 0.411348 0.813953
283 COA 0.411348 0.813953
284 RFL 0.410256 0.855422
285 N01 0.410072 0.945205
286 NWW 0.41 0.774648
287 A6D 0.409836 0.73494
288 CMX 0.409722 0.813953
289 649 0.409091 0.775281
290 4TA 0.408759 0.841463
291 SAH 0.408696 0.75641
292 DSH 0.407407 0.716049
293 NEC 0.407407 0.76
294 CUU 0.40708 0.931507
295 SFG 0.40708 0.763158
296 S7M 0.40678 0.702381
297 SMM 0.40678 0.697674
298 J4G 0.406504 0.907895
299 7C5 0.40625 0.831169
300 8Q2 0.406015 0.804598
301 V3L 0.405172 0.931507
302 DTP 0.405172 0.868421
303 SAM 0.405172 0.702381
304 A3N 0.40367 0.776316
305 IMO 0.40367 0.890411
306 K2R 0.403226 0.893333
307 CAO 0.402778 0.786517
308 AMX 0.402778 0.823529
309 30N 0.402778 0.744681
310 COS 0.402778 0.795455
311 TAP 0.402778 0.896104
312 ZAS 0.401869 0.75641
313 A3S 0.401786 0.824324
314 EEM 0.401709 0.702381
315 BYC 0.401316 0.816092
316 GJV 0.4 0.719512
317 IVC 0.4 0.804598
318 GGZ 0.4 0.814815
319 SCO 0.4 0.813953
320 AMZ 0.4 0.90411
321 S4M 0.4 0.659091
322 6MZ 0.4 0.891892
323 PLP AAD 0.4 0.744444
324 SA8 0.4 0.719512
Similar Ligands (3D)
Ligand no: 1; Ligand: DQV; Similar ligands found: 0
No: Ligand Similarity coefficient
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: 1
This union binding pocket(no: 1) in the query (biounit: 6nrf.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 6W65 T9D 10.3321
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