Receptor
PDB id Resolution Class Description Source Keywords
5XSU 2.4 Å EC: 2.4.2.30 NOVEL ORALLY EFFICACIOUS INHIBITORS COMPLEXED WITH PARP1 HOMO SAPIENS COMPLEX STRUCTURE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DESIGN AND SYNTHESIS OF 2-(4,5,6,7-TETRAHYDROTHIENOPYRIDIN-2-YL)-BENZOIMIDA CARBOXAMIDES AS NOVEL ORALLY EFFICACIOUS POLY(ADP-RIBOSE)POLYMERASE (PARP) INHIBITORS EUR J MED CHEM V. 145 389 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:403;
B:401;
A:402;
D:402;
B:406;
B:403;
B:404;
A:404;
D:401;
A:406;
B:405;
A:401;
C:401;
A:405;
C:402;
B:402;
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;
submit data
96.063 O4 S [O-]S...
8E3 B:407;
A:407;
D:403;
C:403;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 180 nM
300.288 C15 H13 F N4 O2 c1c(c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4PJT 2.35 Å EC: 2.4.2.30 STRUCTURE OF PARP1 CATALYTIC DOMAIN BOUND TO INHIBITOR BMN 6 HOMO SAPIENS PARP1 INHIBITOR COMPLEX TRANSFERASE-TRANSFERASE INHIBITOR
Ref.: STRUCTURAL BASIS FOR THE INHIBITION OF POLY(ADP-RIB POLYMERASES 1 AND 2 BY BMN 673, A POTENT INHIBITOR FROM DIHYDROPYRIDOPHTHALAZINONE. ACTA CRYSTALLOGR.,SECT.F V. 70 1143 2014
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 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....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
16 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
17 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
18 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
19 6I8T - H7Z C21 H29 N3 O2 C[C@@H]1c2....
20 6I8M - H7W C21 H29 N3 O2 C[C@H]1c2c....
21 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
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: 8E3; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 8E3 1 1
2 8EC 0.517647 0.862069
3 8E6 0.494253 0.862069
Similar Ligands (3D)
Ligand no: 1; Ligand: 8E3; Similar ligands found: 248
No: Ligand Similarity coefficient
1 3RL 0.9463
2 MRE 0.9395
3 041 0.9322
4 H32 0.9267
5 697 0.9245
6 OSY 0.9223
7 NU3 0.9213
8 NAR 0.9203
9 LU2 0.9186
10 AV6 0.9155
11 AGI 0.9142
12 1UR 0.9141
13 QUE 0.9127
14 907 0.9114
15 244 0.9113
16 6JP 0.9101
17 1W4 0.9099
18 6X1 0.9097
19 1V8 0.9093
20 MHB 0.9089
21 1V0 0.9085
22 6BK 0.9085
23 334 0.9078
24 STL 0.9077
25 136 0.9076
26 1UT 0.9064
27 5XM 0.9049
28 BZC 0.9043
29 A64 0.9033
30 F36 0.9032
31 79X 0.9030
32 338 0.9029
33 SAK 0.9029
34 RPB 0.9021
35 KUQ 0.9015
36 2ZI 0.9015
37 KVN 0.9011
38 PIT 0.9006
39 8M5 0.9004
40 M16 0.9001
41 O9T 0.8999
42 W2E 0.8995
43 XAV 0.8994
44 J8D 0.8993
45 T5J 0.8989
46 7LU 0.8979
47 245 0.8979
48 68C 0.8978
49 06R 0.8974
50 HWB 0.8969
51 08C 0.8969
52 KVW 0.8963
53 F08 0.8959
54 KVQ 0.8953
55 147 0.8951
56 MYC 0.8951
57 5LP 0.8950
58 29F 0.8946
59 DMB 0.8946
60 O9Z 0.8944
61 C17 0.8937
62 6B5 0.8936
63 OUA 0.8934
64 BUX 0.8933
65 OUG 0.8931
66 KMP 0.8930
67 IMK 0.8928
68 97K 0.8928
69 ECZ 0.8927
70 7GK 0.8925
71 NTI 0.8925
72 0HV 0.8921
73 73E 0.8919
74 5WW 0.8918
75 27F 0.8915
76 DH2 0.8913
77 CWE 0.8912
78 EDZ 0.8909
79 TNC 0.8906
80 8XY 0.8901
81 DQH 0.8897
82 TH1 0.8896
83 S13 0.8896
84 J2W 0.8895
85 BO1 0.8893
86 WG8 0.8891
87 1UZ 0.8890
88 GN5 0.8889
89 196 0.8886
90 IDE 0.8883
91 MR4 0.8882
92 HCC 0.8880
93 J5Z 0.8877
94 G2V 0.8876
95 3TI 0.8873
96 3MI 0.8871
97 83D 0.8871
98 IY5 0.8868
99 28C 0.8866
100 6TJ 0.8866
101 IW3 0.8860
102 P34 0.8850
103 36K 0.8848
104 B1N 0.8848
105 AX1 0.8846
106 OSJ 0.8846
107 B1W 0.8843
108 6MY 0.8842
109 6QX 0.8840
110 C18 0.8838
111 KS2 0.8838
112 M07 0.8836
113 GEN 0.8833
114 PNW 0.8833
115 A63 0.8832
116 1AV 0.8831
117 31F 0.8827
118 O53 0.8827
119 BGC BGC 0.8822
120 123 0.8821
121 FYO 0.8817
122 4B8 0.8817
123 NBZ GLA 0.8816
124 7FZ 0.8814
125 MR5 0.8807
126 SGW 0.8807
127 CT7 0.8800
128 F1T 0.8797
129 3JC 0.8790
130 S06 0.8785
131 ZAR 0.8785
132 O9Q 0.8784
133 BUN 0.8781
134 A45 0.8779
135 HUL 0.8775
136 LJ2 0.8775
137 0O7 0.8772
138 135 0.8772
139 9C8 0.8771
140 T21 0.8771
141 IRH 0.8767
142 BJ4 0.8766
143 91F 0.8764
144 M08 0.8764
145 A26 0.8755
146 TVC 0.8752
147 E9L 0.8752
148 MBE 0.8751
149 OSD 0.8751
150 QC1 0.8746
151 DX8 0.8746
152 5EZ 0.8744
153 OQR 0.8743
154 AOB 0.8743
155 3WL 0.8742
156 CDJ 0.8740
157 J45 0.8740
158 1WZ 0.8740
159 4KN 0.8739
160 1UW 0.8734
161 801 0.8732
162 IW4 0.8731
163 W8L 0.8731
164 IW5 0.8730
165 UAY 0.8729
166 4BE 0.8722
167 57D 0.8719
168 797 0.8716
169 KXN 0.8716
170 H2W 0.8714
171 1UA 0.8714
172 M09 0.8714
173 2UV 0.8711
174 DZ3 0.8711
175 J8G 0.8711
176 NKI 0.8708
177 802 0.8707
178 IIH 0.8703
179 20D 0.8702
180 D64 0.8694
181 KHP 0.8693
182 M3W 0.8693
183 124 0.8692
184 1VG 0.8685
185 EEY 0.8684
186 397 0.8682
187 X8I 0.8680
188 PNG 0.8677
189 NAB 0.8676
190 SDN 0.8674
191 OAK 0.8673
192 ZTW 0.8670
193 F33 0.8667
194 4P9 0.8666
195 5TU 0.8664
196 1V1 0.8661
197 X8E 0.8660
198 CJN 0.8659
199 3Q0 0.8658
200 Q92 0.8658
201 PJK 0.8655
202 39R 0.8654
203 A73 0.8651
204 LZ7 0.8650
205 IZ9 0.8649
206 J2Q 0.8648
207 IDD 0.8646
208 MRI 0.8641
209 S1C 0.8637
210 PNJ 0.8636
211 OAQ 0.8631
212 53X 0.8630
213 ZZ1 GLA 0.8630
214 EBB 0.8627
215 L43 0.8626
216 1NE 0.8625
217 MYU 0.8625
218 6FX 0.8625
219 MT6 0.8622
220 120 0.8618
221 4L2 0.8618
222 8J4 0.8616
223 BMZ 0.8616
224 7G2 0.8616
225 9B2 0.8613
226 6VX 0.8602
227 C3G 0.8601
228 LJ1 0.8598
229 6H2 0.8598
230 609 0.8597
231 D59 0.8596
232 Z3A 0.8589
233 785 0.8587
234 IDZ 0.8584
235 3WK 0.8583
236 VT3 0.8582
237 YEX 0.8579
238 OT4 0.8577
239 BVB 0.8572
240 55H 0.8571
241 0NH 0.8567
242 RNP 0.8560
243 G27 0.8559
244 1R5 0.8558
245 M94 0.8556
246 JKN 0.8547
247 EES 0.8529
248 CR4 0.8528
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 4pjt.bio2) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 6W65 T9D 10.1083
Pocket No.: 2; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 4pjt.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 6W65 T9D 10.1083
Pocket No.: 3; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 4pjt.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 6W65 T9D 10.1083
Pocket No.: 4; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 4pjt.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 3ESS 18N 5.65217
2 6W65 T9D 10.1083
APoc FAQ
Feedback