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;
 Kd = 0.6 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 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: 6C6; Similar ligands found: 146
No: Ligand ECFP6 Tc MDL keys Tc
1 6C6 1 1
2 6MZ 0.696203 0.893333
3 6IA 0.643678 0.875
4 2SA 0.611111 0.896104
5 AMP 0.585366 0.905405
6 A 0.585366 0.905405
7 6K6 0.585106 0.893333
8 IMO 0.564706 0.866667
9 NO7 0.547368 0.848101
10 AMP MG 0.505747 0.866667
11 PGS 0.5 0.804878
12 ITT 0.5 0.855263
13 AP2 0.5 0.896104
14 A12 0.5 0.896104
15 BA3 0.5 0.857143
16 HEJ 0.494624 0.881579
17 ATP 0.494624 0.881579
18 B4P 0.494505 0.857143
19 ADP 0.494505 0.881579
20 AP5 0.494505 0.857143
21 45A 0.494382 0.857143
22 A2D 0.494382 0.857143
23 ABM 0.494382 0.857143
24 25A 0.49 0.881579
25 5FA 0.489362 0.881579
26 AQP 0.489362 0.881579
27 AT4 0.48913 0.848101
28 6MD 0.487805 0.753247
29 AU1 0.483871 0.858974
30 71V 0.483516 0.82716
31 TAT 0.474227 0.848101
32 T99 0.474227 0.848101
33 APC 0.473684 0.896104
34 ADP BEF 0.473118 0.855263
35 ADP MG 0.473118 0.855263
36 AN2 0.473118 0.87013
37 SRA 0.47191 0.858974
38 AGS 0.46875 0.8375
39 ADX 0.468085 0.776471
40 CA0 0.468085 0.835443
41 M33 0.468085 0.846154
42 K2R 0.466667 0.87013
43 N6P 0.466019 0.878378
44 ACP 0.463158 0.883117
45 50T 0.463158 0.87013
46 KG4 0.463158 0.835443
47 6YZ 0.46 0.883117
48 AMZ 0.45977 0.807692
49 ACQ 0.459184 0.883117
50 ANP 0.459184 0.858974
51 APR 0.458333 0.857143
52 G 6MZ C 0.458333 0.818182
53 AR6 0.458333 0.857143
54 PRX 0.458333 0.883117
55 PR8 0.457143 0.911392
56 V2G 0.454545 0.8625
57 8LE 0.454545 0.814815
58 RBY 0.453608 0.871795
59 ADV 0.453608 0.871795
60 ATP MG 0.453608 0.855263
61 ADP PO3 0.453608 0.855263
62 AD9 0.453608 0.858974
63 AIR 0.452381 0.84
64 QA7 0.45098 0.814815
65 8LQ 0.45098 0.848101
66 7RP 0.450549 0.890411
67 ATF 0.45 0.848101
68 ANP MG 0.45 0.846154
69 BEF ADP 0.44898 0.833333
70 P2P 0.445652 0.866667
71 JLN 0.445652 0.807692
72 1RB 0.444444 0.849315
73 C2R 0.443182 0.797468
74 HQG 0.441176 0.87013
75 5AL 0.44 0.846154
76 RBZ 0.43956 0.815789
77 APC MG 0.438776 0.857143
78 JNT 0.438095 0.883117
79 AHX 0.438095 0.839506
80 ARU 0.438095 0.785714
81 MAP 0.436893 0.8375
82 A22 0.436893 0.87013
83 VO4 ADP 0.435644 0.858974
84 ALF ADP 0.435644 0.792683
85 25L 0.435185 0.87013
86 NIA 0.433333 0.75
87 9ZA 0.432692 0.82716
88 8QN 0.432692 0.846154
89 9ZD 0.432692 0.82716
90 SRP 0.431373 0.871795
91 8LH 0.431373 0.825
92 7RA 0.430108 0.893333
93 RMB 0.430108 0.837838
94 FAI 0.430108 0.807692
95 AAM 0.430108 0.905405
96 GAP 0.43 0.8125
97 ADQ 0.428571 0.835443
98 AMO 0.428571 0.871795
99 A3R 0.428571 0.897436
100 A1R 0.428571 0.897436
101 4AD 0.428571 0.860759
102 SON 0.427083 0.896104
103 PTJ 0.425926 0.817073
104 FYA 0.425926 0.92
105 NB8 0.425926 0.839506
106 DLL 0.424528 0.846154
107 ADP BMA 0.420561 0.8125
108 OOB 0.419048 0.846154
109 5SV 0.419048 0.886076
110 OZV 0.419048 0.857143
111 6MA 0.416667 0.906667
112 PAJ 0.415094 0.785714
113 KMQ 0.414414 0.825
114 LMS 0.413043 0.755814
115 TXA 0.412844 0.825
116 BIS 0.412844 0.873418
117 3OD 0.412844 0.835443
118 7MD 0.412281 0.876543
119 00A 0.411215 0.804878
120 XAH 0.410714 0.876543
121 DAL AMP 0.409524 0.822785
122 5GP 0.408163 0.825
123 G 0.408163 0.825
124 OK8 0.407767 0.822785
125 9X8 0.407407 0.814815
126 OAD 0.407407 0.835443
127 3UK 0.407407 0.835443
128 PMO 0.40625 0.815789
129 A3P 0.40625 0.88
130 A2P 0.40625 0.866667
131 O02 0.405941 0.8625
132 JSQ 0.405941 0.8375
133 HFD 0.405941 0.8375
134 LAD 0.40367 0.898734
135 B5V 0.40367 0.825
136 P5A 0.40367 0.797753
137 WAQ 0.40367 0.922078
138 5AS 0.402062 0.733333
139 IMP 0.402062 0.846154
140 ATP A 0.401786 0.844156
141 ATP A A A 0.401786 0.844156
142 FA5 0.401786 0.871795
143 RGT 0.401786 0.848101
144 ME8 0.4 0.831325
145 1ZZ 0.4 0.853659
146 AFH 0.4 0.807229
Similar Ligands (3D)
Ligand no: 1; Ligand: 6C6; 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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