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 21 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 20 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 19 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 9GM 0.663265 0.879518
13 GSP 0.663265 0.858824
14 GP2 0.663158 0.869048
15 FEG 0.642857 0.883721
16 ZGP 0.637168 0.873563
17 Y9Z 0.632075 0.840909
18 G2R 0.631068 0.869048
19 G2P 0.63 0.869048
20 GPG 0.625 0.891566
21 GAV 0.617647 0.869048
22 GDR 0.611111 0.914634
23 GFB 0.611111 0.914634
24 GTG 0.611111 0.892857
25 ALF 5GP 0.61 0.827586
26 G3A 0.605505 0.902439
27 GPD 0.603604 0.882353
28 GKE 0.601852 0.891566
29 GDD 0.601852 0.891566
30 GDC 0.601852 0.891566
31 G5P 0.6 0.902439
32 FE9 0.595041 0.860215
33 JB2 0.594595 0.914634
34 6CK 0.590909 0.870588
35 GDP AF3 0.590476 0.827586
36 GKD 0.580357 0.891566
37 GDP ALF 0.575472 0.827586
38 ALF GDP 0.575472 0.827586
39 GDX 0.575221 0.902439
40 JB3 0.564103 0.926829
41 GMP 0.56044 0.792683
42 U2G 0.546219 0.915663
43 NGD 0.546219 0.891566
44 GDP 7MG 0.54386 0.891566
45 G G 0.539823 0.902439
46 PGD 0.539683 0.904762
47 CG2 0.53719 0.915663
48 2MD 0.532787 0.895349
49 CAG 0.532258 0.842697
50 MGD 0.532258 0.895349
51 G3D 0.523364 0.888889
52 TPG 0.51938 0.88764
53 MD1 0.515625 0.895349
54 G4P 0.513761 0.888889
55 3GP 0.51 0.876543
56 0O2 0.508929 0.888889
57 DBG 0.496183 0.880952
58 G4M 0.492754 0.863636
59 A G 0.492063 0.890244
60 U A G G 0.488189 0.890244
61 2GP 0.480392 0.865854
62 G A A A 0.480315 0.879518
63 GCP G 0.478261 0.853659
64 AKW 0.472 0.850575
65 GH3 0.464286 0.878049
66 BGO 0.460317 0.880952
67 GPX 0.45614 0.853659
68 G1G 0.454545 0.904762
69 G1R G1R 0.451852 0.858824
70 GPC 0.450382 0.883721
71 GGM 0.449612 0.860465
72 DGI 0.449541 0.835294
73 PGD O 0.448529 0.855556
74 DGT 0.446429 0.835294
75 G U 0.445312 0.903614
76 IDP 0.444444 0.876543
77 P2G 0.443396 0.819277
78 P1G 0.435185 0.809524
79 DGP 0.433962 0.845238
80 DG 0.433962 0.845238
81 R7I 0.428571 0.853659
82 MGP 0.428571 0.891566
83 R5I 0.428571 0.853659
84 G C 0.427481 0.903614
85 6G0 0.424779 0.891566
86 IMP 0.424528 0.8875
87 G7M 0.420561 0.902439
88 GTA 0.416 0.892857
89 APC G U 0.414815 0.845238
90 G G G RPC 0.406015 0.879518
91 35G 0.401786 0.8875
92 PCG 0.401786 0.8875
93 C2E 0.401786 0.876543
Ligand no: 2; Ligand: GDP; Similar ligands found: 161
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 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3WB0; Ligand: FEG; 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: 3wb0.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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