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;
Kd = 2.6 uM
417.354 C15 H24 N5 O7 P CC(C)...
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 9 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Kd = 2.6 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Kd = 0.6 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Kd = 0.8 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 8 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Kd = 2.6 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Kd = 0.6 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Kd = 0.8 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 6 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Kd = 2.6 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Kd = 0.6 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Kd = 0.8 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 (2D)
Ligand no: 1; Ligand: 6IA; Similar ligands found: 168
No: Ligand ECFP6 Tc MDL keys Tc
1 6IA 1 1
2 6MZ 0.730769 0.871795
3 6K6 0.666667 0.896104
4 6C6 0.643678 0.875
5 2SA 0.622222 0.851852
6 NO7 0.608696 0.851852
7 A 0.578313 0.858974
8 AMP 0.578313 0.858974
9 IMO 0.55814 0.822785
10 6MD 0.518519 0.759494
11 PGS 0.51087 0.767442
12 45A 0.505618 0.860759
13 ABM 0.505618 0.860759
14 QA7 0.50505 0.864198
15 ADP 0.48913 0.8375
16 A2D 0.488889 0.814815
17 PRX 0.484211 0.8625
18 AMP MG 0.483146 0.822785
19 5AL 0.479592 0.82716
20 AU1 0.478723 0.817073
21 ITT 0.478723 0.8125
22 M33 0.478723 0.82716
23 71V 0.478261 0.788235
24 A12 0.478261 0.829268
25 AP2 0.478261 0.829268
26 BA3 0.478261 0.814815
27 7RP 0.477778 0.844156
28 8LQ 0.475248 0.851852
29 ATP 0.473684 0.8375
30 50T 0.473684 0.82716
31 HEJ 0.473684 0.8375
32 AP5 0.473118 0.814815
33 B4P 0.473118 0.814815
34 9ZD 0.470588 0.831325
35 25A 0.470588 0.8375
36 9ZA 0.470588 0.831325
37 8LH 0.47 0.851852
38 5FA 0.46875 0.8375
39 APC 0.46875 0.829268
40 G 6MZ C 0.46875 0.8
41 AQP 0.46875 0.8375
42 AT4 0.468085 0.807229
43 AN2 0.468085 0.82716
44 SRA 0.466667 0.817073
45 AIR 0.464286 0.797468
46 ADX 0.463158 0.741573
47 CA0 0.463158 0.795181
48 K2R 0.462264 0.82716
49 AHX 0.461538 0.821429
50 N6P 0.461538 0.833333
51 XAH 0.458716 0.835294
52 ACP 0.458333 0.839506
53 KG4 0.458333 0.795181
54 8QN 0.456311 0.82716
55 5SV 0.456311 0.843373
56 HY8 0.45614 0.732558
57 TAT 0.454545 0.807229
58 AMZ 0.454545 0.768293
59 ANP 0.454545 0.817073
60 T99 0.454545 0.807229
61 ACQ 0.454545 0.839506
62 AR6 0.453608 0.814815
63 APR 0.453608 0.814815
64 ADP MG 0.452632 0.8125
65 ADP BEF 0.452632 0.8125
66 4AD 0.451923 0.819277
67 8LE 0.45 0.841463
68 V2G 0.45 0.843373
69 AGS 0.44898 0.797619
70 RBY 0.44898 0.807229
71 ADV 0.44898 0.807229
72 AD9 0.44898 0.817073
73 PTJ 0.448598 0.865854
74 TXA 0.448598 0.807229
75 JNT 0.447619 0.839506
76 ARU 0.447619 0.833333
77 YLP 0.447368 0.837209
78 DAL AMP 0.446602 0.804878
79 ANP MG 0.445545 0.804878
80 BEF ADP 0.444444 0.792683
81 NIA 0.444444 0.715909
82 SRP 0.441176 0.851852
83 6YZ 0.441176 0.839506
84 AAM 0.44086 0.858974
85 RMB 0.44086 0.818182
86 LAD 0.439252 0.855422
87 HZ2 0.438596 0.732558
88 C2R 0.438202 0.759036
89 PAJ 0.438095 0.855422
90 AMO 0.438095 0.829268
91 HQG 0.436893 0.82716
92 TT8 0.436893 0.72619
93 YLB 0.435897 0.858824
94 1ZZ 0.435185 0.813953
95 FYA 0.435185 0.85
96 ME8 0.435185 0.857143
97 NB8 0.435185 0.8
98 RBZ 0.434783 0.820513
99 ADP PO3 0.434343 0.8125
100 ATP MG 0.434343 0.8125
101 APC MG 0.434343 0.792683
102 ARG AMP 0.433628 0.825581
103 A22 0.432692 0.82716
104 MAP 0.432692 0.797619
105 ATF 0.431373 0.807229
106 6MA 0.427083 0.8375
107 5AS 0.427083 0.73913
108 WAQ 0.425926 0.809524
109 GAP 0.425743 0.817073
110 P2P 0.425532 0.822785
111 7RA 0.425532 0.848101
112 JLN 0.425532 0.768293
113 FAI 0.425532 0.768293
114 A1R 0.424528 0.853659
115 ADQ 0.424528 0.817073
116 LMS 0.423913 0.722222
117 1RB 0.423913 0.805195
118 YLC 0.423729 0.857143
119 3US 0.422764 0.793103
120 SON 0.42268 0.829268
121 48N 0.422414 0.8
122 AYB 0.421488 0.848837
123 7MD 0.421053 0.835294
124 DLL 0.420561 0.804878
125 TSB 0.419048 0.717391
126 MTP 0.418605 0.690476
127 MYR AMP 0.418182 0.793103
128 VO4 ADP 0.417476 0.817073
129 ALF ADP 0.417476 0.755814
130 A5A 0.417476 0.725275
131 OK8 0.417476 0.783133
132 IOT 0.416667 0.827586
133 9X8 0.416667 0.797619
134 OAD 0.416667 0.817073
135 PMO 0.416667 0.797468
136 OZV 0.415094 0.814815
137 OOB 0.415094 0.804878
138 AP0 0.411765 0.8
139 7MC 0.411765 0.837209
140 A3R 0.411215 0.853659
141 LSS 0.411215 0.78022
142 KMQ 0.410714 0.829268
143 B5M 0.410714 0.797619
144 54H 0.409524 0.747253
145 VMS 0.409524 0.747253
146 52H 0.409524 0.73913
147 3OD 0.409091 0.817073
148 1PR 0.409091 0.776471
149 BIS 0.409091 0.809524
150 GA7 0.408696 0.875
151 NVA LMS 0.407407 0.752688
152 00A 0.407407 0.767442
153 36A 0.40678 0.704545
154 F2R 0.406504 0.837209
155 25L 0.405405 0.82716
156 5GP 0.40404 0.785714
157 G 0.40404 0.785714
158 LEU LMS 0.40367 0.769231
159 3UK 0.40367 0.795181
160 ADP BMA 0.40367 0.795181
161 3DH 0.402174 0.728395
162 A2P 0.402062 0.822785
163 A3P 0.402062 0.835443
164 9SN 0.401786 0.758621
165 YLA 0.401639 0.816092
166 B5V 0.4 0.785714
167 J4G 0.4 0.864198
168 PR8 0.4 0.845238
Similar Ligands (3D)
Ligand no: 1; Ligand: 6IA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4kxl.bio2) has 49 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4kxl.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: 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 Sequence Similarity
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