Receptor
PDB id Resolution Class Description Source Keywords
1A26 2.25 Å EC: 2.4.2.30 THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH CARBA-NAD GALLUS GALLUS TRANSFERASE GLYCOSYLTRANSFERASE NAD(+) ADP- RIBOSYLTRANSFERASE
Ref.: THE MECHANISM OF THE ELONGATION AND BRANCHING REACTION OF POLY(ADP-RIBOSE) POLYMERASE AS DERIVED FROM CRYSTAL STRUCTURES AND MUTAGENESIS. J.MOL.BIOL. V. 278 57 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CNA A:200;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
662.46 C22 H30 N7 O13 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1EFY 2.2 Å EC: 2.4.2.30 CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF POLY (ADP- RIBOSE) POLYMERASE COMPLEXED WITH A BENZIMIDAZOLE INHIBITOR GALLUS GALLUS CRYSTAL STRUCTURE BENZIMIDAZOLE INHIBITOR CATALYTIC FRAGMENT POLYMERASE TRANSFERASE
Ref.: RESISTANCE-MODIFYING AGENTS. 9. SYNTHESIS AND BIOLOGICAL PROPERTIES OF BENZIMIDAZOLE INHIBITORS OF THE DNA REPAIR ENZYME POLY(ADP-RIBOSE) POLYMERASE. J.MED.CHEM. V. 43 4084 2000
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
2 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
3 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
4 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
5 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
2 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
3 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
4 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
5 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
6 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
7 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
8 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
9 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
10 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
11 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
2 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
3 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
4 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
5 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
6 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
7 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
8 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
9 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
10 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
11 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
12 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
13 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
14 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
15 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
16 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
17 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
18 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
19 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
20 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
21 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
22 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
23 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
24 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
25 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
26 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CNA; Similar ligands found: 212
No: Ligand ECFP6 Tc MDL keys Tc
1 CNA 1 1
2 DND 0.644068 0.972973
3 NXX 0.644068 0.972973
4 NAD 0.642276 0.972603
5 A2D 0.62 0.958904
6 NAD IBO 0.608 0.909091
7 BA3 0.607843 0.958904
8 A3D 0.606299 0.959459
9 AP5 0.601942 0.958904
10 B4P 0.601942 0.958904
11 M33 0.590476 0.92
12 ATP 0.584906 0.932432
13 5FA 0.579439 0.932432
14 AQP 0.579439 0.932432
15 AR6 0.579439 0.932432
16 APR 0.579439 0.932432
17 3OD 0.577586 0.933333
18 SAP 0.574074 0.884615
19 AGS 0.574074 0.884615
20 OAD 0.573913 0.933333
21 ADP 0.571429 0.932432
22 ACP 0.570093 0.907895
23 CA0 0.560748 0.933333
24 NAJ PYZ 0.559702 0.8875
25 AD9 0.559633 0.907895
26 A1R 0.556522 0.897436
27 ACQ 0.54955 0.907895
28 5AL 0.544643 0.92
29 ABM 0.542857 0.881579
30 GTA 0.540323 0.9
31 NAX 0.539683 0.911392
32 A22 0.53913 0.945946
33 DLL 0.538462 0.945946
34 00A 0.538462 0.897436
35 1ZZ 0.537815 0.831325
36 PRX 0.536364 0.858974
37 ANP 0.535714 0.907895
38 ADX 0.53211 0.841463
39 A 0.528846 0.905405
40 AMP 0.528846 0.905405
41 NAI 0.527559 0.922078
42 TXD 0.527559 0.922078
43 50T 0.527273 0.894737
44 ATF 0.526316 0.896104
45 SRP 0.521739 0.921053
46 NAP 0.521739 0.959459
47 NHD 0.518797 0.945946
48 4AD 0.516949 0.96
49 PAJ 0.516949 0.875
50 ADQ 0.516949 0.933333
51 NAQ 0.514493 0.910256
52 AHX 0.512605 0.910256
53 NFD 0.511111 0.922078
54 ZID 0.510791 0.959459
55 AMP NAD 0.510791 0.921053
56 SON 0.509091 0.896104
57 APC 0.508929 0.896104
58 25L 0.508197 0.945946
59 NAE 0.507246 0.934211
60 AMP MG 0.504673 0.881579
61 A12 0.504587 0.896104
62 AP2 0.504587 0.896104
63 AMO 0.504202 0.946667
64 PR8 0.504132 0.864198
65 DZD 0.503704 0.898734
66 TXA 0.5 0.921053
67 PTJ 0.5 0.8625
68 FA5 0.5 0.946667
69 BIS 0.5 0.873418
70 ME8 0.5 0.853659
71 FYA 0.5 0.92
72 T5A 0.496241 0.878049
73 8ID 0.496183 0.923077
74 AP0 0.496183 0.886076
75 TAT 0.495652 0.896104
76 GAP 0.495652 0.907895
77 SRA 0.495327 0.858974
78 NA0 0.492958 0.946667
79 A4P 0.492424 0.857143
80 UP5 0.492308 0.934211
81 LAD 0.491803 0.875
82 AU1 0.491071 0.907895
83 ADP MG 0.491071 0.894737
84 LAQ 0.488372 0.831325
85 G3A 0.488189 0.910256
86 YAP 0.488 0.934211
87 NB8 0.487805 0.910256
88 ADP BEF 0.486726 0.871795
89 BEF ADP 0.486726 0.871795
90 N01 0.485507 0.945946
91 COD 0.485294 0.825581
92 AFH 0.484375 0.875
93 G5P 0.484375 0.910256
94 XAH 0.484127 0.853659
95 25A 0.483333 0.932432
96 NDC 0.482993 0.910256
97 EAD 0.482517 0.911392
98 NDE 0.479452 0.946667
99 ADP PO3 0.478261 0.931507
100 ADV 0.478261 0.896104
101 RBY 0.478261 0.896104
102 NJP 0.477941 0.96
103 IOT 0.477612 0.823529
104 DAL AMP 0.475 0.92
105 NAD NDT 0.475 0.739583
106 ATP MG 0.474138 0.894737
107 139 0.474074 0.911392
108 ADJ 0.474074 0.865854
109 4TC 0.473684 0.910256
110 MYR AMP 0.472 0.831325
111 P1H 0.469388 0.888889
112 NGD 0.466667 0.923077
113 NAD TDB 0.466258 0.705882
114 TYM 0.466165 0.946667
115 MAP 0.46281 0.884615
116 ALF ADP 0.462185 0.860759
117 ADP ALF 0.462185 0.860759
118 YLP 0.462121 0.833333
119 BT5 0.460432 0.823529
120 NAJ 0.459854 0.945946
121 ANP MG 0.458333 0.884615
122 ADP VO4 0.458333 0.92
123 M24 0.457746 0.864198
124 TAP 0.455172 0.897436
125 YLC 0.451852 0.853659
126 YLB 0.451852 0.833333
127 7MD 0.450382 0.876543
128 ADP BMA 0.448 0.933333
129 AMP DBH 0.446154 0.907895
130 FB0 0.443709 0.797753
131 NAJ PZO 0.443662 0.886076
132 AHZ 0.443609 0.831325
133 0WD 0.442857 0.910256
134 A2R 0.442623 0.92
135 54H 0.442623 0.781609
136 VMS 0.442623 0.781609
137 7MC 0.441176 0.855422
138 PAP 0.440678 0.918919
139 ITT 0.439655 0.88
140 TSB 0.439024 0.811765
141 AYB 0.438849 0.823529
142 A5A 0.438017 0.8
143 AOC 0.4375 0.789474
144 YLY 0.4375 0.823529
145 G5A 0.436975 0.793103
146 TAD 0.43609 0.875
147 AVV 0.435484 0.8625
148 5AS 0.434783 0.752809
149 3AT 0.433333 0.906667
150 BTX 0.432624 0.833333
151 2A5 0.432203 0.858974
152 LSS 0.432 0.775281
153 DSZ 0.432 0.813953
154 YLA 0.431655 0.833333
155 NPW 0.431655 0.9
156 52H 0.430894 0.772727
157 ATP A A A 0.430769 0.945205
158 UPA 0.430657 0.922078
159 6AD 0.429752 0.851852
160 LPA AMP 0.42963 0.831325
161 N0B 0.428571 0.855422
162 ATR 0.428571 0.905405
163 53H 0.427419 0.772727
164 6FA 0.425806 0.855422
165 ODP 0.425532 0.923077
166 LEU LMS 0.425197 0.795455
167 NA7 0.425197 0.896104
168 ALF ADP 3PG 0.423358 0.851852
169 LA8 ALF 3PG 0.423358 0.851852
170 SSA 0.422764 0.813953
171 MTA 0.422018 0.74359
172 P5A 0.421875 0.758242
173 NDO 0.421769 0.933333
174 NDP 0.421429 0.910256
175 NSS 0.420635 0.835294
176 FAD 0.420382 0.865854
177 FAS 0.420382 0.865854
178 5N5 0.419048 0.786667
179 TXP 0.41844 0.910256
180 NZQ 0.41844 0.898734
181 NVA LMS 0.417323 0.795455
182 EP4 0.416667 0.725
183 5CA 0.416 0.813953
184 5CD 0.415094 0.773333
185 3DH 0.414414 0.74359
186 A3P 0.413793 0.905405
187 RAB 0.413462 0.810811
188 XYA 0.413462 0.810811
189 ADN 0.413462 0.810811
190 AF3 ADP 3PG 0.413043 0.851852
191 DTA 0.412844 0.779221
192 4TA 0.412587 0.865854
193 SFD 0.411392 0.747368
194 3AM 0.410714 0.866667
195 F2N 0.410714 0.827586
196 FDA 0.410256 0.825581
197 FNK 0.409938 0.818182
198 DTP 0.409836 0.87013
199 AR6 AR6 0.407407 0.932432
200 P5F 0.407186 0.837209
201 PPS 0.406504 0.819277
202 ARU 0.40625 0.807229
203 YSA 0.406015 0.813953
204 AV2 0.403226 0.857143
205 A4D 0.401869 0.786667
206 ETB 0.401361 0.825581
207 DCA 0.401361 0.816092
208 KAA 0.4 0.766667
209 SMM 0.4 0.72093
210 M2T 0.4 0.728395
211 FA9 0.4 0.878049
212 GSU 0.4 0.793103
Similar Binding Sites
Pocket no: 1; Query (leader) PDB : 1EFY; Ligand: BZC; Similar sites found: 96
This union binding pocket (no: 1) in the query (biounit: 1efy.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 1EFY BZC 5.218e-15 1
2 4PJT 2YQ 4.566e-09 0.76727
3 4GV4 MEJ 2.347e-09 0.75372
4 3KJD 78P 1.317e-09 0.73827
5 4MSG 2C6 6.148e-08 0.70291
6 4BUY F37 1.412e-07 0.69114
7 4J3L AJ5 4.187e-08 0.68697
8 4L0T 1V0 5.151e-08 0.68602
9 3ESS 18N 1.393e-07 0.65714
10 3SE2 3AB 6.239e-07 0.63134
11 3SE2 LDR 6.541e-07 0.63031
12 3Q9O NAD 2.396e-06 0.60757
13 3B82 NAD 2.827e-06 0.59822
14 1XK9 P34 1.03e-05 0.56989
15 1OG1 TAD 0.0001336 0.50843
16 1GZF NAD 0.000973 0.47838
17 1GZF ADP 0.00123 0.47314
18 2A5F NAD 0.0009564 0.46579
19 1Q19 APC 0.001635 0.45877
20 1OJZ NAD 0.003163 0.43987
21 4F0E 0RU 0.0004412 0.43246
22 1DTP APU 0.005608 0.42744
23 1KOR ANP 0.02233 0.42309
24 1U1F 183 0.04607 0.41603
25 1CT9 AMP 0.007658 0.41597
26 4H03 NAD 0.009224 0.41436
27 1NW4 IMH 0.00837 0.41406
28 4FK7 P34 9.649e-05 0.41104
29 3VZS CAA 0.04906 0.41061
30 1LVG 5GP 0.01135 0.40987
31 1REQ DCA 0.04449 0.40954
32 1TRD PGH 0.01095 0.40829
33 2BO4 FLC 0.02231 0.40804
34 3ABI NAD 0.03103 0.40743
35 4KXL 6C6 0.04878 0.40732
36 2YPI PGA 0.01049 0.40668
37 4QAR ADE 0.01181 0.40668
38 1SW0 PGA 0.01287 0.40482
39 3QPB R1P 0.01644 0.40403
40 1JR8 FAD 0.02635 0.4027
41 3FIU AMP 0.01169 0.4017
42 3EUF BAU 0.01656 0.40169
43 2BVN ENX 0.02051 0.40121
44 2A8Y MTA 0.0216 0.40007
45 3LGS ADE 0.01859 0.39918
46 2XIQ MLC 0.03777 0.39895
47 1ODJ GMP 0.01706 0.39875
48 1CT9 IUM 0.01718 0.39861
49 4UUG PXG 0.02976 0.39834
50 4A0S NAP 0.04681 0.39662
51 4DSU BZI 0.004259 0.39396
52 3PT9 SAH 0.02968 0.39305
53 4CE5 PDG 0.03232 0.39303
54 4EWN 0VR 0.01888 0.39155
55 4P5E N6P 0.03525 0.39109
56 3BJE R1P 0.0299 0.39092
57 1SVM ATP 0.04178 0.39068
58 2GJN FMN 0.04623 0.38996
59 4FXQ G9L 0.005661 0.38914
60 1G51 AMP 0.003141 0.38788
61 2A9K NAD 0.03806 0.38754
62 2J41 5GP 0.02583 0.38742
63 4EAR IM5 0.03223 0.3872
64 1G2O IMH 0.03276 0.38684
65 2F6U CIT 0.01039 0.38639
66 4BMX ADE 0.04003 0.38449
67 2P4S DIH 0.03336 0.38425
68 1EX7 5GP 0.02013 0.38289
69 1O94 AMP 0.04777 0.38248
70 3LF0 ATP 0.04829 0.38223
71 1MMQ RRS 0.04206 0.38136
72 2WSI FAD 0.04674 0.38106
73 1NQ7 ARL 0.03663 0.3799
74 1QD0 RR6 0.02401 0.37984
75 3DP9 BIG 0.04652 0.37914
76 2MJP ANP 0.03712 0.37713
77 1VMK GUN 0.012 0.3751
78 3JU6 ANP 0.01942 0.37497
79 2X6M ASP 0.01558 0.37084
80 1MRE GDP 0.04863 0.36507
81 2HO2 PRO 0.009125 0.36173
82 2XG5 EC5 0.01672 0.36124
83 2XQ0 BES 0.04238 0.36083
84 2QHV OC9 0.04473 0.35883
85 2X1L MET 0.04727 0.3584
86 2XG5 EC2 0.006275 0.35813
87 4KYQ FLC 0.02046 0.3578
88 2FKA BEF 0.002905 0.35749
89 2XOM GAL 0.002946 0.35742
90 2G30 ALA 0.003649 0.35556
91 3PPQ CHT 0.02302 0.34869
92 1C3X 8IG 0.02272 0.34864
93 2P9T 3PG 0.03776 0.34134
94 1OFL NGK 0.04953 0.33693
95 3ZFZ 1W8 0.01997 0.33677
96 3A16 PXO 0.04655 0.3278
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