Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6C6 D:201;
C:201;
B:201;
A:201;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 1.2 uM
415.338 C15 H22 N5 O7 P c1nc(...
SO4 D:202;
C:202;
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
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: 6C6; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 6C6 1 1
2 6IA 0.643678 0.875
3 2SA 0.611111 0.896104
4 AMP 0.585366 0.905405
5 A 0.585366 0.905405
6 6K6 0.585106 0.893333
7 IMO 0.564706 0.866667
8 AP2 0.5 0.896104
9 ITT 0.5 0.855263
10 PGS 0.5 0.804878
11 AMP MG 0.5 0.833333
12 BA3 0.5 0.857143
13 A12 0.5 0.896104
14 ATP 0.494624 0.881579
15 AP5 0.494505 0.857143
16 B4P 0.494505 0.857143
17 ADP 0.494505 0.881579
18 A2D 0.494382 0.857143
19 ABM 0.494382 0.857143
20 25A 0.49 0.881579
21 AQP 0.489362 0.881579
22 5FA 0.489362 0.881579
23 6MD 0.487805 0.753247
24 AU1 0.483871 0.858974
25 71V 0.483516 0.82716
26 TAT 0.474227 0.848101
27 APC 0.473684 0.896104
28 AN2 0.473118 0.87013
29 SRA 0.47191 0.858974
30 SAP 0.46875 0.8375
31 AGS 0.46875 0.8375
32 CA0 0.468085 0.835443
33 M33 0.468085 0.846154
34 ADX 0.468085 0.776471
35 ADP MG 0.468085 0.822785
36 N6P 0.466019 0.878378
37 50T 0.463158 0.87013
38 BEF ADP 0.463158 0.802469
39 ACP 0.463158 0.883117
40 ADP BEF 0.463158 0.802469
41 AMZ 0.45977 0.807692
42 ACQ 0.459184 0.883117
43 ANP 0.459184 0.858974
44 PRX 0.458333 0.883117
45 AR6 0.458333 0.857143
46 APR 0.458333 0.857143
47 PR8 0.457143 0.911392
48 ADV 0.453608 0.871795
49 ADP PO3 0.453608 0.855263
50 RBY 0.453608 0.871795
51 AD9 0.453608 0.858974
52 AIR 0.452381 0.84
53 7RP 0.450549 0.890411
54 ATF 0.45 0.848101
55 ATP MG 0.44898 0.822785
56 P2P 0.445652 0.866667
57 JLN 0.445652 0.807692
58 ANP MG 0.445545 0.814815
59 1RB 0.444444 0.849315
60 C2R 0.443182 0.797468
61 5AL 0.44 0.846154
62 RBZ 0.43956 0.815789
63 ARU 0.438095 0.785714
64 AHX 0.438095 0.839506
65 A22 0.436893 0.87013
66 MAP 0.436893 0.8375
67 ADP ALF 0.435644 0.792683
68 ALF ADP 0.435644 0.792683
69 25L 0.435185 0.87013
70 NIA 0.433333 0.75
71 8QN 0.432692 0.846154
72 SRP 0.431373 0.871795
73 VO4 ADP 0.431373 0.846154
74 ADP VO4 0.431373 0.846154
75 7RA 0.430108 0.893333
76 RMB 0.430108 0.837838
77 FAI 0.430108 0.807692
78 AAM 0.430108 0.905405
79 GAP 0.43 0.8125
80 A1R 0.428571 0.897436
81 ADQ 0.428571 0.835443
82 AMO 0.428571 0.871795
83 4AD 0.428571 0.860759
84 SON 0.427083 0.896104
85 NB8 0.425926 0.839506
86 PTJ 0.425926 0.817073
87 FYA 0.425926 0.92
88 DLL 0.424528 0.846154
89 ADP BMA 0.420561 0.8125
90 OOB 0.419048 0.846154
91 5SV 0.419048 0.886076
92 PAJ 0.415094 0.785714
93 BIS 0.412844 0.873418
94 3OD 0.412844 0.835443
95 TXA 0.412844 0.825
96 7MD 0.412281 0.876543
97 00A 0.411215 0.804878
98 XAH 0.410714 0.876543
99 DAL AMP 0.409524 0.822785
100 G 0.408163 0.825
101 5GP 0.408163 0.825
102 OAD 0.407407 0.835443
103 3UK 0.407407 0.835443
104 A2P 0.40625 0.866667
105 A3P 0.40625 0.88
106 PMO 0.40625 0.815789
107 WAQ 0.40367 0.922078
108 LAD 0.40367 0.898734
109 A A 0.40367 0.881579
110 P5A 0.40367 0.797753
111 IMP 0.402062 0.846154
112 5AS 0.402062 0.733333
113 YAP 0.401786 0.860759
114 ATP A A A 0.401786 0.844156
115 FA5 0.401786 0.871795
116 RGT 0.401786 0.848101
117 AFH 0.4 0.807229
118 ME8 0.4 0.831325
119 1ZZ 0.4 0.853659
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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