Receptor
PDB id Resolution Class Description Source Keywords
4KXM 2.24 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH N6-ISOPENTENYL-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
6IA C:201;
B:201;
D:201;
A:201;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ki = 3.3 uM
417.354 C15 H24 N5 O7 P CC(C)...
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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: 6IA; Similar ligands found: 138
No: Ligand ECFP6 Tc MDL keys Tc
1 6IA 1 1
2 6K6 0.666667 0.896104
3 6C6 0.643678 0.875
4 2SA 0.622222 0.851852
5 AMP 0.578313 0.858974
6 A 0.578313 0.858974
7 IMO 0.55814 0.822785
8 6MD 0.518519 0.759494
9 PGS 0.51087 0.767442
10 ABM 0.505618 0.860759
11 ADP 0.48913 0.8375
12 A2D 0.488889 0.814815
13 PRX 0.484211 0.8625
14 5AL 0.479592 0.82716
15 AU1 0.478723 0.817073
16 ITT 0.478723 0.8125
17 M33 0.478723 0.82716
18 BA3 0.478261 0.814815
19 AP2 0.478261 0.829268
20 A12 0.478261 0.829268
21 71V 0.478261 0.788235
22 7RP 0.477778 0.844156
23 AMP MG 0.477778 0.792683
24 50T 0.473684 0.82716
25 ATP 0.473684 0.8375
26 B4P 0.473118 0.814815
27 AP5 0.473118 0.814815
28 25A 0.470588 0.8375
29 AQP 0.46875 0.8375
30 5FA 0.46875 0.8375
31 APC 0.46875 0.829268
32 AN2 0.468085 0.82716
33 SRA 0.466667 0.817073
34 AIR 0.464286 0.797468
35 CA0 0.463158 0.795181
36 ADX 0.463158 0.741573
37 AHX 0.461538 0.821429
38 N6P 0.461538 0.833333
39 XAH 0.458716 0.835294
40 ACP 0.458333 0.839506
41 8QN 0.456311 0.82716
42 5SV 0.456311 0.843373
43 ANP 0.454545 0.817073
44 TAT 0.454545 0.807229
45 AMZ 0.454545 0.768293
46 ACQ 0.454545 0.839506
47 AR6 0.453608 0.814815
48 APR 0.453608 0.814815
49 4AD 0.451923 0.819277
50 AD9 0.44898 0.817073
51 RBY 0.44898 0.807229
52 ADV 0.44898 0.807229
53 AGS 0.44898 0.797619
54 SAP 0.44898 0.797619
55 TXA 0.448598 0.807229
56 PTJ 0.448598 0.865854
57 ADP MG 0.447917 0.783133
58 ARU 0.447619 0.833333
59 YLP 0.447368 0.837209
60 DAL AMP 0.446602 0.804878
61 NIA 0.444444 0.715909
62 BEF ADP 0.443299 0.764706
63 ADP BEF 0.443299 0.764706
64 ANP MG 0.441176 0.776471
65 SRP 0.441176 0.851852
66 AAM 0.44086 0.858974
67 RMB 0.44086 0.818182
68 LAD 0.439252 0.855422
69 C2R 0.438202 0.759036
70 PAJ 0.438095 0.855422
71 AMO 0.438095 0.829268
72 TT8 0.436893 0.72619
73 YLB 0.435897 0.858824
74 NB8 0.435185 0.8
75 FYA 0.435185 0.85
76 ME8 0.435185 0.857143
77 1ZZ 0.435185 0.813953
78 RBZ 0.434783 0.820513
79 ADP PO3 0.434343 0.8125
80 MAP 0.432692 0.797619
81 A22 0.432692 0.82716
82 ATF 0.431373 0.807229
83 ATP MG 0.43 0.783133
84 5AS 0.427083 0.73913
85 WAQ 0.425926 0.809524
86 GAP 0.425743 0.817073
87 P2P 0.425532 0.822785
88 JLN 0.425532 0.768293
89 7RA 0.425532 0.848101
90 FAI 0.425532 0.768293
91 ADQ 0.424528 0.817073
92 A1R 0.424528 0.853659
93 1RB 0.423913 0.805195
94 YLC 0.423729 0.857143
95 3US 0.422764 0.793103
96 SON 0.42268 0.829268
97 48N 0.422414 0.8
98 AYB 0.421488 0.848837
99 7MD 0.421053 0.835294
100 DLL 0.420561 0.804878
101 TSB 0.419048 0.717391
102 MTP 0.418605 0.690476
103 MYR AMP 0.418182 0.793103
104 ADP ALF 0.417476 0.755814
105 A5A 0.417476 0.725275
106 ALF ADP 0.417476 0.755814
107 IOT 0.416667 0.827586
108 LEU LMS 0.416667 0.76087
109 OAD 0.416667 0.817073
110 PMO 0.416667 0.797468
111 OOB 0.415094 0.804878
112 ARG AMP 0.413793 0.825581
113 ADP VO4 0.413462 0.804878
114 VO4 ADP 0.413462 0.804878
115 7MC 0.411765 0.837209
116 AP0 0.411765 0.8
117 LSS 0.411215 0.78022
118 VMS 0.409524 0.747253
119 54H 0.409524 0.747253
120 52H 0.409524 0.73913
121 BIS 0.409091 0.809524
122 1PR 0.409091 0.776471
123 3OD 0.409091 0.817073
124 00A 0.407407 0.767442
125 NVA LMS 0.407407 0.741935
126 36A 0.40678 0.704545
127 25L 0.405405 0.82716
128 5GP 0.40404 0.785714
129 G 0.40404 0.785714
130 ADP BMA 0.40367 0.795181
131 3UK 0.40367 0.795181
132 3DH 0.402174 0.728395
133 A2P 0.402062 0.822785
134 A3P 0.402062 0.835443
135 9SN 0.401786 0.758621
136 YLA 0.401639 0.816092
137 PR8 0.4 0.845238
138 A A 0.4 0.8375
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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