Receptor
PDB id Resolution Class Description Source Keywords
4F97 2.11 Å EC: 2.4.-.- CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, I WITH GDP AND VALIDOXYLAMINE A 7'-PHOSPHATE STREPTOMYCES HYGROSCOPICUS SUBSP. LIMOORGANISM_TAXID: 264445 TWIN ROSSMAN FOLD TRANSFERASE
Ref.: MECHANISTIC INSIGHTS INTO VALIDOXYLAMINE A 7'-PHOSP SYNTHESIS BY VLDE USING THE STRUCTURE OF THE ENTIRE COMPLEX. PLOS ONE V. 7 44934 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:504;
B:504;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
EDO A:503;
B:503;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GDP A:501;
B:502;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
VDO A:502;
B:501;
Valid;
Valid;
none;
none;
submit data
415.33 C14 H26 N O11 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4F97 2.11 Å EC: 2.4.-.- CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, I WITH GDP AND VALIDOXYLAMINE A 7'-PHOSPHATE STREPTOMYCES HYGROSCOPICUS SUBSP. LIMOORGANISM_TAXID: 264445 TWIN ROSSMAN FOLD TRANSFERASE
Ref.: MECHANISTIC INSIGHTS INTO VALIDOXYLAMINE A 7'-PHOSP SYNTHESIS BY VLDE USING THE STRUCTURE OF THE ENTIRE COMPLEX. PLOS ONE V. 7 44934 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4F97 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4F96 - GDP C10 H15 N5 O11 P2 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 3 families.
1 4F97 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4F96 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4F97 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4F96 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; 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
Ligand no: 2; Ligand: VDO; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 VDO 1 1
2 VDM 0.65625 0.77551
3 CAK 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4F97; Ligand: GDP; Similar sites found: 30
This union binding pocket(no: 1) in the query (biounit: 4f97.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.001114 0.45067 None
2 1UO5 PIH 0.01583 0.43461 None
3 3RV5 DXC 0.01449 0.42238 None
4 4X7R UDP 0.0006733 0.42243 1.21704
5 2GEK GDP 0.001706 0.43974 1.97044
6 1OUK 084 0.04135 0.43366 2.18579
7 3QCJ NX4 0.02463 0.40075 2.58065
8 3OKA GDD 0.00001415 0.53412 2.88714
9 4MRP GSH 0.008984 0.42298 2.9316
10 4E90 7RG 0.01496 0.40339 3.03951
11 3OKP GDD 0.00001069 0.51347 3.04569
12 4A0M NAD 0.03535 0.40253 3.42742
13 4NES UDP 0.002285 0.44074 3.47594
14 3AQT RCO 0.009947 0.41698 3.67347
15 1RZU ADP 0.00003263 0.5172 3.91753
16 4MGA 27L 0.01783 0.40237 3.92157
17 2IV3 UDP 0.0001019 0.51028 4.38596
18 3BEO UDP 0.001624 0.41474 4.8
19 4XSU UDP 0.0005547 0.48414 5.41237
20 4XSU GLC 0.0005547 0.48414 5.41237
21 3KP6 SAL 0.01425 0.41563 5.96026
22 1QM5 PLP 0.02055 0.42518 6.23742
23 5JFL NAD 0.01276 0.42051 6.23742
24 5ENZ UDP 0.001206 0.41093 8.2495
25 4UCC ZKW 0.01632 0.41224 9.01288
26 4LH7 NMN 0.003607 0.43638 10.2167
27 4O4Z N2O 0.01312 0.40248 14.2857
28 2F2G HMH 0.01376 0.40111 16.7421
29 2WTX VDO 0.000007288 0.589 27.5654
30 2WTX UDP 0.000008504 0.58895 27.5654
Pocket No.: 2; Query (leader) PDB : 4F97; Ligand: VDO; 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: 4f97.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4F97; Ligand: GDP; 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: 4f97.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4F97; Ligand: VDO; Similar sites found: 28
This union binding pocket(no: 4) in the query (biounit: 4f97.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.00981 0.4279 None
2 4X7R 3YW 0.00005301 0.47821 1.21704
3 4X7R UDP 0.004195 0.42163 1.21704
4 4PQG NAG 0.001771 0.46601 2.61569
5 3OKA GDD 0.00005588 0.40329 2.88714
6 1TZD ADP 0.02633 0.41601 2.90909
7 3OKP GDD 0.00008121 0.51468 3.04569
8 2IW1 U2F 0.000159 0.45554 3.47594
9 2XA2 UPG 0.0003493 0.46106 3.84615
10 1RZU ADP 0.0002223 0.50563 3.91753
11 2QZS GLC 0.000008312 0.40721 4.12371
12 2QZS 250 0.000008312 0.40721 4.12371
13 2QZS ADP 0.000008312 0.40721 4.12371
14 3NB0 G6P 0.006036 0.43876 4.22535
15 3BEO UDP 0.008353 0.41518 4.8
16 4XSU GLC 0.00004878 0.47114 5.41237
17 4XSU UDP 0.0001077 0.45789 5.41237
18 1EM6 NBG 0.0009828 0.44398 5.4326
19 2YRX AMP 0.02781 0.41059 5.9867
20 1QM5 PLP 0.0001446 0.48077 6.23742
21 1QM5 GLC GLC GLC PO4 SGC GLC 0.001768 0.42443 6.23742
22 5C79 PBU 0.02308 0.41566 6.66667
23 5ENZ UDP 0.008226 0.41193 8.2495
24 1DCP HBI 0.04387 0.4032 10.5769
25 2F2G HMH 0.03034 0.40454 16.7421
26 1A5V Y3 0.01605 0.42173 20.8861
27 2WTX VDO 0.0000000002139 0.69824 27.5654
28 2WTX UDP 0.0000000003427 0.6949 27.5654
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