Receptor
PDB id Resolution Class Description Source Keywords
5LDQ 1.7 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF E.COLI LIGT COMPLEXED WITH NADP+ ESCHERICHIA COLI BL21(DE3) ENZYME 2H PHOSPHOESTERASE/LIGASE HYDROLASE
Ref.: STRUCTURAL ASPECTS OF NUCLEOTIDE LIGAND BINDING BY BACTERIAL 2H PHOSPHOESTERASE. PLOS ONE V. 12 70355 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP D:201;
C:201;
A:202;
A:201;
B:201;
Valid;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.438;
Atoms found MORE than expected: % Diff = 2;
Atoms found LESS than expected: % Diff = 0.354;
Atoms found MORE than expected: % Diff = 2;
none;
Kd = 40 uM
743.405 C21 H28 N7 O17 P3 c1cc(...
PO4 D:202;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
CL C:202;
A:203;
B:202;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
1PE B:203;
A:204;
C:203;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
238.278 C10 H22 O6 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LDQ 1.7 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF E.COLI LIGT COMPLEXED WITH NADP+ ESCHERICHIA COLI BL21(DE3) ENZYME 2H PHOSPHOESTERASE/LIGASE HYDROLASE
Ref.: STRUCTURAL ASPECTS OF NUCLEOTIDE LIGAND BINDING BY BACTERIAL 2H PHOSPHOESTERASE. PLOS ONE V. 12 70355 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5LDM Kd = 140 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
2 5LDP Kd = 70 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 5LDQ Kd = 40 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 5LDK Kd = 70 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5LDM Kd = 140 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
2 5LDP Kd = 70 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 5LDQ Kd = 40 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 5LDK Kd = 70 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5LDM Kd = 140 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
2 5LDP Kd = 70 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 5LDQ Kd = 40 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 5LDK Kd = 70 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LDQ; Ligand: NAP; Similar sites found: 16
This union binding pocket(no: 1) in the query (biounit: 5ldq.bio4) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GQG DCD 0.02824 0.40359 2.82486
2 1YQZ FAD 0.04429 0.42403 3.38983
3 5MW8 ATP 0.02429 0.40454 3.38983
4 2XMI FLC 0.00002838 0.55318 3.9548
5 4YNU LGC 0.03315 0.42787 3.9548
6 4OCJ NDG 0.04631 0.40419 4.51977
7 2CM4 RCL 0.01048 0.42296 4.66667
8 2VFK AMP 0.0001834 0.49556 5.08475
9 5JJ2 MLI 0.000001427 0.46598 5.08475
10 4K3H 1OM 0.005909 0.43877 5.08475
11 5I0U DCY 0.003892 0.43496 5.08475
12 4IGQ THR M3L GLN 0.02572 0.40321 5.08475
13 5FLJ QUE 0.02685 0.40247 5.64972
14 5F3I 5UJ 0.004605 0.47969 8.47458
15 5JSP DQY 0.01074 0.40335 13.5593
16 5A3T MMK 0.004411 0.45945 24.2938
Pocket No.: 2; Query (leader) PDB : 5LDQ; Ligand: NAP; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 5ldq.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DSU BZI 0.01149 0.41585 None
2 2VDF OCT 0.02283 0.41932 2.25989
3 2PT9 2MH 0.02992 0.40381 3.38983
4 5ALC TIQ 0.01176 0.41696 4.51977
5 1VJ7 GDP 0.01299 0.40697 7.34463
6 5HCF BGC 0.03426 0.40317 7.34463
7 5TH5 MET 0.02032 0.40057 9.60452
8 4I54 1C1 0.02813 0.40072 10.1695
9 4YVN EBS 0.0035 0.43873 18.0791
Pocket No.: 3; Query (leader) PDB : 5LDQ; Ligand: NAP; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 5ldq.bio3) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WN5 MVC 0.01657 0.41476 None
2 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 0.0001291 0.40679 None
3 2OQ2 A3P 0.02965 0.40004 6.21469
4 1ZB6 GST 0.03689 0.40463 6.77966
5 2QM9 TDZ 0.01885 0.41025 7.74194
6 2UUU FAD 0.04286 0.42133 7.9096
7 2UUU PL3 0.04286 0.42133 7.9096
8 2Z77 HE7 0.02665 0.40082 11.5108
9 5LRT ADP 0.02615 0.40739 11.8644
10 2RKV ZBA 0.02697 0.41963 12.4294
11 2RKV COA 0.02364 0.41963 12.4294
12 5U98 1KX 0.02383 0.42546 21.2121
Pocket No.: 4; Query (leader) PDB : 5LDQ; Ligand: NAP; 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: 5ldq.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5LDQ; Ligand: NAP; Similar sites found: 2
This union binding pocket(no: 5) in the query (biounit: 5ldq.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3W9F I3P 0.03565 0.40941 3.38983
2 5FJJ MAN 0.01115 0.46405 7.34463
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