Receptor
PDB id Resolution Class Description Source Keywords
5xsr 2.3 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
8EC A:401;
Valid;
none;
Kd = 0.000000064 M
316.353 C15 H13 F N4 O S c1c(c...
SO4 A:403;
A:404;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
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: 8EC; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 8EC 1 1
2 8E6 0.723684 1
3 8E3 0.517647 0.862069
Similar Ligands (3D)
Ligand no: 1; Ligand: 8EC; Similar ligands found: 164
No: Ligand Similarity coefficient
1 3RL 0.9495
2 MRE 0.9357
3 H32 0.9227
4 041 0.9208
5 697 0.9204
6 NU3 0.9177
7 LU2 0.9173
8 C17 0.9166
9 OSY 0.9142
10 1W4 0.9133
11 AGI 0.9116
12 J8D 0.9112
13 PIT 0.9109
14 NAR 0.9094
15 1UR 0.9086
16 907 0.9084
17 AV6 0.9075
18 7GK 0.9071
19 6JP 0.9062
20 1UT 0.9056
21 STL 0.9055
22 136 0.9052
23 6BK 0.9043
24 F08 0.9041
25 334 0.9022
26 M16 0.9015
27 5LP 0.9013
28 MHB 0.9007
29 1V0 0.9006
30 3TI 0.9000
31 RPB 0.8998
32 1V8 0.8998
33 2ZI 0.8996
34 1WZ 0.8996
35 QUE 0.8990
36 J2W 0.8986
37 SAK 0.8982
38 S16 0.8974
39 68C 0.8974
40 F36 0.8972
41 6X1 0.8970
42 79X 0.8959
43 A64 0.8947
44 AX1 0.8941
45 5XM 0.8939
46 IW3 0.8938
47 C18 0.8931
48 97K 0.8918
49 W2E 0.8918
50 8M5 0.8913
51 O9T 0.8911
52 06R 0.8910
53 338 0.8909
54 LJ2 0.8907
55 8XY 0.8903
56 9C8 0.8894
57 CWE 0.8894
58 O9Z 0.8893
59 KVN 0.8891
60 HCC 0.8884
61 HWB 0.8883
62 08C 0.8880
63 G2V 0.8877
64 6B5 0.8873
65 XAV 0.8870
66 5WW 0.8866
67 IY5 0.8862
68 KMP 0.8855
69 L43 0.8855
70 244 0.8855
71 KUQ 0.8850
72 3JD 0.8847
73 OUG 0.8845
74 OUA 0.8845
75 KVW 0.8840
76 27F 0.8840
77 29F 0.8839
78 IDE 0.8836
79 NTI 0.8835
80 FYO 0.8833
81 6QX 0.8829
82 3MI 0.8826
83 MYC 0.8826
84 P34 0.8826
85 WG8 0.8825
86 S13 0.8825
87 DX8 0.8822
88 IW5 0.8820
89 AOB 0.8820
90 NNF 0.8818
91 1VG 0.8816
92 68Q 0.8802
93 5EZ 0.8802
94 BUN 0.8801
95 IW4 0.8799
96 B1N 0.8798
97 31F 0.8798
98 DMB 0.8795
99 F1T 0.8795
100 B1W 0.8795
101 KS2 0.8790
102 TNC 0.8788
103 7LU 0.8787
104 BVB 0.8783
105 1UZ 0.8783
106 KVQ 0.8779
107 245 0.8777
108 1UA 0.8775
109 GN5 0.8772
110 DQH 0.8770
111 O9Q 0.8768
112 ECZ 0.8766
113 BGC BGC 0.8765
114 OSJ 0.8765
115 797 0.8763
116 4BE 0.8757
117 8J4 0.8755
118 A63 0.8753
119 T5J 0.8748
120 EBB 0.8744
121 F33 0.8742
122 M07 0.8741
123 OQR 0.8740
124 DZ3 0.8737
125 IZ9 0.8732
126 6MY 0.8731
127 BUX 0.8730
128 135 0.8724
129 O53 0.8721
130 A26 0.8715
131 LZ7 0.8711
132 123 0.8691
133 802 0.8688
134 0O7 0.8686
135 OSD 0.8685
136 LJ1 0.8683
137 7FC 0.8682
138 S06 0.8677
139 TH1 0.8670
140 S1C 0.8665
141 M09 0.8663
142 E9L 0.8663
143 KXN 0.8652
144 9B2 0.8650
145 4AJ 0.8649
146 J2Q 0.8643
147 OAQ 0.8641
148 1AV 0.8628
149 BO1 0.8626
150 CTI 0.8626
151 9AW 0.8622
152 1UW 0.8606
153 397 0.8605
154 3K1 0.8601
155 97Z 0.8600
156 9EG 0.8592
157 A92 0.8584
158 BCE 0.8578
159 HUL 0.8570
160 XEB 0.8569
161 SNP 0.8566
162 M85 0.8552
163 55H 0.8524
164 B1K 0.8518
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
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