Receptor
PDB id Resolution Class Description Source Keywords
4KXN 1.9 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH KINETINE RIBOSIDE MONO RATTUS NORVEGICUS DEOXYRIBONUCLEOSIDE 5-prime -MONOPHOSPHATE N-GLYCOSIDASE HYDROLAS
Ref.: N (6)-SUBSTITUTED AMPS INHIBIT MAMMALIAN DEOXYNUCLE N-HYDROLASE DNPH1. PLOS ONE V. 8 80755 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6K6 B:201;
D:201;
A:201;
C:201;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 1.8 uM
427.306 C15 H18 N5 O8 P c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KXL 1.69 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH 6-CYCLOPENTYL-AMP RATTUS NORVEGICUS DEOXYRIBONUCLEOSIDE 5-prime -MONOPHOSPHATE N-GLYCOSIDASE HYDROLAS
Ref.: N (6)-SUBSTITUTED AMPS INHIBIT MAMMALIAN DEOXYNUCLE N-HYDROLASE DNPH1. PLOS ONE V. 8 80755 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Ki = 3.3 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Ki = 1.2 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Ki = 1.8 uM 6K6 C15 H18 N5 O8 P c1cc(oc1)C....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Ki = 3.3 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Ki = 1.2 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Ki = 1.8 uM 6K6 C15 H18 N5 O8 P c1cc(oc1)C....
5 4P5E Ki = 2.8 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Ki = 3.3 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Ki = 1.2 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Ki = 1.8 uM 6K6 C15 H18 N5 O8 P c1cc(oc1)C....
5 4P5E Ki = 2.8 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6K6; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 6K6 1 1
2 6IA 0.666667 0.896104
3 6C6 0.585106 0.893333
4 2SA 0.56701 0.893333
5 AMP 0.539326 0.957143
6 A 0.539326 0.957143
7 IMO 0.521739 0.915493
8 N6P 0.476636 0.928571
9 ITT 0.464646 0.902778
10 PGS 0.464646 0.846154
11 AU1 0.464646 0.905405
12 AMP MG 0.463158 0.878378
13 50T 0.46 0.917808
14 ADP 0.459184 0.930556
15 A2D 0.458333 0.90411
16 ABM 0.458333 0.90411
17 25A 0.457944 0.930556
18 APC 0.455446 0.893333
19 6MD 0.449438 0.819444
20 A12 0.44898 0.893333
21 BA3 0.44898 0.90411
22 AP2 0.44898 0.893333
23 71V 0.44898 0.87013
24 ACP 0.445545 0.905405
25 ATP 0.445545 0.930556
26 AP5 0.444444 0.90411
27 B4P 0.444444 0.90411
28 ACQ 0.442308 0.905405
29 5FA 0.441176 0.930556
30 AQP 0.441176 0.930556
31 AN2 0.44 0.917808
32 SRA 0.4375 0.905405
33 ADX 0.435644 0.814815
34 ADP MG 0.435644 0.866667
35 M33 0.435644 0.891892
36 CA0 0.435644 0.88
37 36A 0.433333 0.710843
38 TAT 0.428571 0.893333
39 WAQ 0.428571 0.846154
40 ANP 0.428571 0.905405
41 APR 0.427184 0.90411
42 PRX 0.427184 0.88
43 AR6 0.427184 0.90411
44 1RB 0.427083 0.898551
45 C2R 0.425532 0.84
46 1ZZ 0.424779 0.804878
47 FYA 0.424779 0.891892
48 5AL 0.424528 0.891892
49 DLL 0.423423 0.891892
50 AHX 0.423423 0.858974
51 ADV 0.423077 0.868421
52 RBY 0.423077 0.868421
53 AD9 0.423077 0.905405
54 SAP 0.423077 0.881579
55 AGS 0.423077 0.881579
56 ATF 0.420561 0.893333
57 ATP MG 0.419048 0.866667
58 7RP 0.418367 0.942029
59 OOB 0.418182 0.891892
60 AIR 0.417582 0.887324
61 BEF ADP 0.417476 0.844156
62 ADP BEF 0.417476 0.844156
63 SRP 0.416667 0.893333
64 ANP MG 0.416667 0.857143
65 GAP 0.415094 0.905405
66 4AD 0.414414 0.857143
67 AMO 0.414414 0.868421
68 RMB 0.414141 0.885714
69 JLN 0.414141 0.851351
70 NB8 0.412281 0.835443
71 PTJ 0.412281 0.858974
72 ARU 0.410714 0.848101
73 AMZ 0.410526 0.851351
74 ADP PO3 0.409524 0.902778
75 MAP 0.409091 0.881579
76 A22 0.409091 0.917808
77 ADP ALF 0.407407 0.833333
78 ALF ADP 0.407407 0.833333
79 3UK 0.40708 0.88
80 AMP DBH 0.40678 0.855263
81 5SV 0.405405 0.835443
82 8QN 0.405405 0.891892
83 LAD 0.403509 0.871795
84 NIA 0.402062 0.7875
85 A1R 0.401786 0.894737
86 ADQ 0.401786 0.905405
87 PAJ 0.401786 0.848101
88 FA5 0.401709 0.868421
89 7RA 0.4 0.943662
90 AAM 0.4 0.957143
91 BIS 0.4 0.87013
92 FAI 0.4 0.851351
93 P2P 0.4 0.915493
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4kxl.bio2) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 4kxl.bio2) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VWA PTY 0.003295 0.48812 None
2 3RV5 DXC 0.04293 0.4448 None
3 2Q37 3AL 0.02545 0.43023 4.60526
4 3B9Z CO2 0.04846 0.43942 5.26316
5 3E7S AT2 0.02669 0.42754 5.92105
6 3R75 PYR 0.04715 0.41542 7.23684
7 3TL1 JRO 0.03018 0.42488 10.5263
8 4RF7 ARG 0.04954 0.40412 11.1842
9 2FJK 13P 0.0488 0.40588 14.4737
10 2F64 12Q 0.0084 0.41859 17.7632
Pocket No.: 3; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found: 4
This union binding pocket(no: 3) in the query (biounit: 4kxl.bio1) has 52 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WUW TSU 0.03024 0.41521 None
2 3M0J OAF 0.01894 0.42707 1.97368
3 3MBI HSX 0.04271 0.41179 3.94737
4 2JCB ADP 0.03024 0.41272 6.57895
Pocket No.: 4; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4kxl.bio1) has 52 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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