Receptor
PDB id Resolution Class Description Source Keywords
3N1S 1.45 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF WILD TYPE ECHINT GMP COMPLEX ESCHERICHIA COLI HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN HINT GMP HYDRO
Ref.: PROBING THE IMPACT OF THE ECHINT C-TERMINAL DOMAIN STRUCTURE AND CATALYSIS. J.MOL.BIOL. V. 404 627 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:201;
B:200;
E:203;
F:202;
I:205;
J:204;
M:207;
N:206;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
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none;
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none;
none;
none;
none;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
EDO A:120;
A:121;
A:122;
B:120;
B:121;
B:122;
B:123;
B:124;
B:125;
E:120;
F:120;
I:120;
I:121;
I:122;
I:123;
J:120;
J:121;
M:120;
M:121;
N:120;
N:121;
N:122;
N:123;
N:124;
N:125;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
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submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3N1S 1.45 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF WILD TYPE ECHINT GMP COMPLEX ESCHERICHIA COLI HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN HINT GMP HYDRO
Ref.: PROBING THE IMPACT OF THE ECHINT C-TERMINAL DOMAIN STRUCTURE AND CATALYSIS. J.MOL.BIOL. V. 404 627 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3N1T - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3N1S - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3N1T - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3N1S - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 5IPC Kd = 13 uM 6CE C20 H24 N7 O6 P S c1ccc2c(c1....
2 4EQG - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 5I2E Kd = 0.23 uM 67D C23 H23 N7 O7 S c1ccc2c(c1....
4 3O1C - ADN C10 H13 N5 O4 c1nc(c2c(n....
5 5IPE - 6CG C10 H14 N5 O7 P S c1nc2c(n1[....
6 4RHN - RIB C5 H10 O5 C([C@@H]1[....
7 3O1X - ADN C10 H13 N5 O4 c1nc(c2c(n....
8 4ZKL - JB6 C24 H34 N10 O13 P2 S2 c1nc(c2c(n....
9 3QGZ - ADN C10 H13 N5 O4 c1nc(c2c(n....
10 5I2F - BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
11 1KPF - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 4EQH - WSA C21 H24 N8 O7 S c1ccc2c(c1....
13 1RZY Ki = 1.25 uM 5AS C12 H18 N6 O6 S CCNS(=O)(=....
14 4EQE - KAA C16 H26 N8 O7 S c1nc(c2c(n....
15 3RHN - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
16 5RHN - 8BR C10 H13 Br N5 O7 P c1nc(c2c(n....
17 3N1T - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
18 3N1S - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
19 4INI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: 63
This union binding pocket(no: 1) in the query (biounit: 3n1s.bio4) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SQL GUN 0.003205 0.44166 None
2 3OCP CMP 0.003231 0.4267 None
3 1N07 ADP 0.005818 0.41887 None
4 4CUB GAL NAG 0.008055 0.41432 None
5 4BTV RB3 0.001619 0.40012 None
6 4JGP PYR 0.0002755 0.43697 2.52101
7 4JOB TLA 0.001506 0.43083 3.36134
8 5UR1 YY9 0.03883 0.40371 3.36134
9 3IT7 TLA 0.00516 0.42583 4.20168
10 4LWU 20U 0.002189 0.42218 4.70588
11 1YQC GLV 0.001605 0.46369 5.04202
12 3ZW2 GLA NAG GAL FUC 0.002351 0.43531 5.04202
13 3ZW2 NAG GAL FUC 0.001496 0.43087 5.04202
14 1SAY PYR 0.01758 0.41548 5.04202
15 1M0W ANP 0.008024 0.40616 5.04202
16 1S68 AMP 0.003654 0.40162 5.04202
17 5F90 GLA GAL BGC 5VQ 0.00864 0.42148 5.88235
18 5F90 GLA GAL 0.008749 0.42106 5.88235
19 5F90 LMR 0.00817 0.41697 5.88235
20 4OCJ NDG 0.03171 0.40454 5.88235
21 5BV3 M7G 0.000003401 0.57089 6.72269
22 3EWK FAD 0.002566 0.43561 7.56302
23 5COU ATP 0.002576 0.43127 7.56302
24 5LRT ADP 0.01344 0.40991 7.56302
25 1N0U SO1 0.01122 0.40541 7.56302
26 5TDF ADP 0.01355 0.40332 7.56302
27 4AVB CMP 0.009524 0.40046 7.56302
28 3X01 AMP 0.001387 0.459 8.40336
29 4FGC PQ0 0.002286 0.44748 8.40336
30 2HGS ADP 0.008897 0.41544 8.40336
31 2ZQO NGA 0.01185 0.41188 8.40336
32 5MW8 ATP 0.01775 0.40102 8.40336
33 2PT9 2MH 0.03403 0.40097 8.40336
34 1UPR 4IP 0.02144 0.41418 9.2437
35 2QQD AG2 0.01723 0.40084 9.2437
36 1UNQ 4IP 0.01615 0.40591 9.6
37 5IQD GNP 0.01238 0.42423 10.084
38 5IQD RIO 0.01299 0.42423 10.084
39 5GVL GI8 0.03207 0.40712 10.084
40 5GVL PLG 0.03207 0.40712 10.084
41 3SXF BK5 0.02491 0.40676 10.084
42 3BF8 MLA 0.01554 0.40042 10.9244
43 2TPS TPS 0.002108 0.45046 11.7647
44 3VSV XYS 0.006474 0.43013 11.7647
45 3ETH ATP 0.01009 0.41115 11.7647
46 3HAV ATP 0.001416 0.40565 11.7647
47 4OGN 2U5 0.008129 0.41202 12.381
48 3BL7 DD1 0.001442 0.4406 12.605
49 4ANW O92 0.01248 0.4195 12.605
50 1ST0 GTG 0.000009674 0.41333 12.605
51 4LH7 1X8 0.00292 0.44756 13.4454
52 2VPQ ANP 0.0112 0.41065 14.2857
53 3PUR 2HG 0.01423 0.40654 14.2857
54 3ANY 2A3 0.00604 0.41679 15.126
55 5CDH TLA 0.0008464 0.44323 15.9664
56 5VZ0 ADP 0.003089 0.4087 18.4874
57 5AVF TAU 0.0007455 0.4624 20.1681
58 3CQL NDG 0.01662 0.40054 22.6891
59 4ASE AV9 0.02415 0.40026 26.0504
60 2Q4H AMP 0.00000002053 0.69589 28.5714
61 4MOB COA 0.01473 0.40798 28.5714
62 5FIT AP2 0.0000000004345 0.73665 31.9328
63 3FHI ANP 0.02256 0.40037 33.6134
Pocket No.: 2; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3n1s.bio4) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3n1s.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: 10
This union binding pocket(no: 4) in the query (biounit: 3n1s.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OBT SLB 0.004705 0.42146 2.52101
2 5JKG 6LF 0.03066 0.40197 4.20168
3 1UH4 GLC GLC GLC GLC GLC 0.01687 0.40538 5.04202
4 4OCV ANP 0.007488 0.4097 5.88235
5 5MUA GAL 0.01332 0.40411 6.72269
6 1NBU PH2 0.005542 0.40491 10.084
7 5N53 8NB 0.01886 0.40314 10.9244
8 4EN4 ATP 0.03376 0.40084 10.9244
9 4EN4 GT0 0.03376 0.40084 10.9244
10 4EN4 GT1 0.03376 0.40084 10.9244
Pocket No.: 5; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: 9
This union binding pocket(no: 5) in the query (biounit: 3n1s.bio3) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1N07 FMN 0.01598 0.41533 None
2 4C2V YJA 0.0058 0.43473 4.20168
3 4IGH 1EA 0.0322 0.42291 5.04202
4 4IGH FMN 0.0322 0.42291 5.04202
5 4IGH ORO 0.0322 0.42291 5.04202
6 5UIU 8CG 0.0273 0.40254 5.88235
7 4U0I 0LI 0.02514 0.40316 11.7647
8 4AT0 FAD 0.04713 0.4049 19.3277
9 2DKH 3HB 0.03994 0.40219 19.3277
Pocket No.: 6; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3n1s.bio3) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: 8
This union binding pocket(no: 7) in the query (biounit: 3n1s.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TY5 ADP 0.00534 0.41017 4.20168
2 2VUT NAD 0.0145 0.40156 6.72269
3 5HVJ ANP 0.009449 0.41586 8.40336
4 5DA3 58V 0.01163 0.40271 9.2437
5 2QLU ADE 0.007291 0.41564 12.605
6 2IVD ACJ 0.0128 0.40073 15.126
7 1O9U ADZ 0.002117 0.42316 21.0084
8 4YMJ 4EJ 0.01761 0.4027 26.8908
Pocket No.: 8; Query (leader) PDB : 3N1S; Ligand: 5GP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 3n1s.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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