Receptor
PDB id Resolution Class Description Source Keywords
4P5D 2.11 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE- MONOPHOSPHATE RATTUS NORVEGICUS N-GLYCOSIDASE INHIBITOR HYDROLASE
Ref.: 6-(HETERO)ARYLPURINE NUCLEOTIDES AS INHIBITORS OF T ONCOGENIC TARGET DNPH1: SYNTHESIS, STRUCTURAL STUDI CYTOTOXIC ACTIVITIES. EUR.J.MED.CHEM. V. 85C 418 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
N6P A:201;
C:201;
Valid;
Valid;
none;
none;
Ki = 1.5 uM
458.361 C20 H19 N4 O7 P c1ccc...
SO4 A:202;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
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: N6P; Similar ligands found: 81
No: Ligand ECFP6 Tc MDL keys Tc
1 N6P 1 1
2 AMP 0.527473 0.942029
3 A 0.527473 0.942029
4 IMO 0.526882 0.955882
5 ITT 0.5 0.942029
6 ATP 0.48 0.915493
7 ADP 0.479592 0.915493
8 6K6 0.476636 0.928571
9 5FA 0.475248 0.915493
10 AQP 0.475248 0.915493
11 PGS 0.47 0.855263
12 71V 0.469388 0.855263
13 2SA 0.466667 0.878378
14 6C6 0.466019 0.878378
15 B4P 0.464646 0.915493
16 AP5 0.464646 0.915493
17 A2D 0.463918 0.915493
18 25A 0.462963 0.942857
19 6IA 0.461538 0.833333
20 BA3 0.454545 0.915493
21 ABM 0.44898 0.888889
22 TAT 0.447619 0.878378
23 ACQ 0.447619 0.890411
24 APC 0.446602 0.878378
25 AN2 0.445545 0.902778
26 ADX 0.441176 0.8
27 M33 0.441176 0.876712
28 CA0 0.441176 0.864865
29 AP2 0.44 0.878378
30 A12 0.44 0.878378
31 AMP MG 0.438776 0.863014
32 3UK 0.4375 0.890411
33 50T 0.436893 0.902778
34 ACP 0.436893 0.890411
35 OOB 0.436364 0.902778
36 RMB 0.434343 0.925373
37 ANP 0.433962 0.890411
38 1RB 0.43299 0.939394
39 PRX 0.432692 0.864865
40 APR 0.432692 0.888889
41 AR6 0.432692 0.888889
42 5AL 0.429907 0.876712
43 AGS 0.428571 0.866667
44 SAP 0.428571 0.866667
45 SRA 0.428571 0.890411
46 AD9 0.428571 0.890411
47 DLL 0.428571 0.902778
48 A22 0.427273 0.929577
49 AU1 0.427184 0.890411
50 25L 0.426087 0.929577
51 ATF 0.425926 0.878378
52 ADQ 0.419643 0.890411
53 RGT 0.418803 0.878378
54 FYA 0.417391 0.902778
55 ARU 0.415929 0.833333
56 ADV 0.415094 0.853333
57 RBY 0.415094 0.853333
58 ADP MG 0.413462 0.851351
59 8QN 0.410714 0.876712
60 7RP 0.41 0.984848
61 BEF ADP 0.409524 0.828947
62 ADP BEF 0.409524 0.828947
63 SRP 0.409091 0.853333
64 PR8 0.408696 0.8
65 AIR 0.408602 0.871429
66 V3L 0.407407 0.915493
67 A1R 0.40708 0.831169
68 PAJ 0.40708 0.810127
69 FA5 0.40678 0.878378
70 PTJ 0.405172 0.844156
71 6AD 0.40367 0.833333
72 00A 0.403509 0.855263
73 6V0 0.403226 0.844156
74 C2R 0.402062 0.824324
75 AMZ 0.402062 0.835616
76 ADP PO3 0.401869 0.887324
77 MAP 0.401786 0.866667
78 4UV 0.4 0.866667
79 RBZ 0.4 0.898551
80 G 0.4 0.853333
81 5GP 0.4 0.853333
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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