Receptor
PDB id Resolution Class Description Source Keywords
3WB2 2.44 Å EC: 2.7.7.- HCGB FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH THE PYRIDINOL PRODUCT IN A MODEL REACTION OF [FE]-HYDROGENASE CB IOSYNTHESIS METHANOCALDOCOCCUS JANNASCHII GTP-BINDING DOMAIN GUANYLYLTRANSFERASE TRANSFERASE
Ref.: IDENTIFICATION OF THE HCGB ENZYME IN [FE]-HYDROGENASE-COFACTOR BIOSYNTHESIS. ANGEW.CHEM.INT.ED.ENGL. V. 52 12555 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YGP A:201;
C:202;
C:201;
A:202;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
484.357 C17 H21 N6 O9 P CC1=C...
MG A:203;
A:205;
Invalid;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
GDP A:204;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WB0 1.91 Å EC: 2.7.7.- HCGB FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH LIGH DECOMPOSED FEGP COFACTOR OF [FE]-HYDROGENASE METHANOCALDOCOCCUS JANNASCHII GTP-BINDING DOMAIN GUANYLYLTRANSFERASE TRANSFERASE
Ref.: IDENTIFICATION OF THE HCGB ENZYME IN [FE]-HYDROGENASE-COFACTOR BIOSYNTHESIS. ANGEW.CHEM.INT.ED.ENGL. V. 52 12555 2013
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3WB2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WB0 - FEG C19 H23 N6 O11 P Cc1c(nc(c(....
3 5D5Q - 57O C9 H11 N O4 Cc1c(nc(c(....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3WB2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WB0 - FEG C19 H23 N6 O11 P Cc1c(nc(c(....
3 5D5Q - 57O C9 H11 N O4 Cc1c(nc(c(....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3WB2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WB0 - FEG C19 H23 N6 O11 P Cc1c(nc(c(....
3 5D5Q - 57O C9 H11 N O4 Cc1c(nc(c(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YGP; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 YGP 1 1
2 GP3 0.706522 0.902439
3 GDP 0.698925 0.901235
4 GNH 0.691489 0.890244
5 GCP 0.6875 0.879518
6 G 0.681319 0.9125
7 5GP 0.681319 0.9125
8 GMV 0.677083 0.879518
9 GTP 0.677083 0.901235
10 G1R 0.670103 0.890244
11 GNP 0.663265 0.879518
12 GSP 0.663265 0.858824
13 GP2 0.663158 0.869048
14 FEG 0.642857 0.883721
15 ZGP 0.637168 0.873563
16 Y9Z 0.632075 0.840909
17 G2R 0.631068 0.869048
18 G2P 0.63 0.869048
19 GPG 0.625 0.891566
20 GAV 0.617647 0.869048
21 GDP MG 0.616162 0.857143
22 GFB 0.611111 0.914634
23 GDR 0.611111 0.914634
24 GTG 0.611111 0.892857
25 ALF 5GP 0.61 0.827586
26 GDP BEF 0.61 0.837209
27 G3A 0.605505 0.902439
28 GPD 0.603604 0.882353
29 GCP G 0.601942 0.86747
30 GKE 0.601852 0.891566
31 GDC 0.601852 0.891566
32 GDD 0.601852 0.891566
33 G5P 0.6 0.902439
34 FE9 0.595041 0.860215
35 JB2 0.594595 0.914634
36 BEF GDP 0.592233 0.827586
37 GTP MG 0.592233 0.857143
38 6CK 0.590909 0.870588
39 GDP AF3 0.590476 0.827586
40 GKD 0.580357 0.891566
41 GDP ALF 0.575472 0.827586
42 GDX 0.575221 0.902439
43 JB3 0.564103 0.926829
44 GMP 0.56044 0.792683
45 G G 0.559633 0.890244
46 NGD 0.546219 0.891566
47 U2G 0.546219 0.915663
48 GDP 7MG 0.54386 0.891566
49 I2C FE2 CMO CMO 0.540323 0.897727
50 PGD 0.539683 0.904762
51 CG2 0.53719 0.915663
52 2MD 0.532787 0.895349
53 MGD 0.532258 0.895349
54 CAG 0.532258 0.842697
55 G3D 0.523364 0.888889
56 TPG 0.51938 0.88764
57 MD1 0.515625 0.895349
58 G4P 0.513761 0.888889
59 3GP 0.51 0.876543
60 0O2 0.508929 0.888889
61 DBG 0.496183 0.880952
62 G4M 0.492754 0.863636
63 U A G G 0.488189 0.890244
64 2GP 0.480392 0.865854
65 G A A A 0.480315 0.879518
66 GH3 0.464286 0.878049
67 BGO 0.460317 0.880952
68 GPX 0.45614 0.853659
69 G1G 0.454545 0.904762
70 G1R G1R 0.451852 0.858824
71 GPC 0.450382 0.883721
72 GGM 0.449612 0.860465
73 DGI 0.449541 0.835294
74 PGD O 0.448529 0.855556
75 DGT 0.446429 0.835294
76 IDP 0.444444 0.876543
77 P2G 0.443396 0.819277
78 G G U 0.439024 0.890244
79 P1G 0.435185 0.809524
80 DG 0.433962 0.845238
81 DGP 0.433962 0.845238
82 MGP 0.428571 0.891566
83 G C 0.427481 0.903614
84 6G0 0.424779 0.891566
85 IMP 0.424528 0.8875
86 G7M 0.420561 0.902439
87 GTA 0.416 0.892857
88 U G A 0.414966 0.892857
89 APC G U 0.414815 0.845238
90 G G G RPC 0.406015 0.879518
91 C2E 0.401786 0.876543
92 PCG 0.401786 0.8875
93 35G 0.401786 0.8875
Ligand no: 2; Ligand: GDP; Similar ligands found: 153
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3WB0; Ligand: FEG; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 3wb0.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X1L MET 0.01858 0.41553 4.21687
2 2XG5 EC5 0.01493 0.41561 4.81928
3 2XG5 EC2 0.01493 0.41561 4.81928
4 4RL4 PPV 0.001408 0.48247 5.42169
5 4BGB ADP 0.008969 0.42104 5.42169
6 4CVN ADP 0.02489 0.40707 13.1387
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