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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: 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
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 with APoc: 92
This union binding pocket(no: 1) in the query (biounit: 4f97.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO5 PIH None
2 5ET3 60C None
3 1NU4 MLA None
4 3RV5 DXC None
5 4WG0 CHD None
6 4GU5 FAD 1.00604
7 4X7R 3YW 1.21704
8 4X7R NTO 1.21704
9 4X7R UDP 1.21704
10 3W5N RAM 1.40845
11 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 1.70068
12 6GNF ADP 1.81087
13 2IYA ZIO 1.88679
14 2GEK GDP 1.97044
15 2J4D FAD 2.01207
16 1OUK 084 2.18579
17 3CV3 UDP 2.21675
18 3O01 DXC 2.27273
19 4CDN FO1 2.28216
20 4CDN FAD 2.28216
21 5AAV GW5 2.38095
22 5FPN KYD 2.41449
23 3QCJ NX4 2.58065
24 4PQG UDP 2.61569
25 1GNI OLA 2.61569
26 1DNP FAD 2.76008
27 3OKA GDD 2.88714
28 5XVS UDP 2.90237
29 4MRP GSH 2.9316
30 2GWH PCI 3.02013
31 4I4B NAD 3.03738
32 4E90 7RG 3.03951
33 3OKP GDD 3.04569
34 6CB2 OLC 3.07167
35 5Y79 3PG 3.34347
36 4A0M NAD 3.42742
37 2IW1 U2F 3.47594
38 4NES UDP 3.47594
39 6DIO NAD 3.4965
40 4I6G FAD 3.62173
41 3AQT RCO 3.67347
42 4AF5 CIT 3.68421
43 2XA2 UPG 3.84615
44 1RZU ADP 3.91753
45 4MGA 27L 3.92157
46 2QE4 JJ3 4.03226
47 2QZS ADP 4.12371
48 2QZS 250 4.12371
49 2QZS GLC 4.12371
50 5K0A FAD 4.24242
51 2CIX CEJ 4.34783
52 2IV3 UDP 4.38596
53 3BEO UDP 4.8
54 4I8P NAD 4.82897
55 6EJI UD2 5.36193
56 4XSU UDP 5.41237
57 4XSU GLC 5.41237
58 5U97 PIT 5.6338
59 5A4W QCT 5.66038
60 6GL8 F3Q 5.81395
61 5XJD 87L 5.90909
62 3KP6 SAL 5.96026
63 6FBA D48 6.01719
64 1NP7 FAD 6.13497
65 1QM5 PLP 6.23742
66 5JFL NAD 6.23742
67 4OAS 2SW 6.25
68 3RUU 37G 6.9869
69 5C9J DAO 7.11744
70 5LX9 OLB 7.74648
71 5ENZ UDP 8.2495
72 3H0A D30 8.45588
73 4UCC ZKW 9.01288
74 2VZZ SCA 9.17431
75 1R6N 434 9.95261
76 2OI9 GLN LEU SER PRO PHE PRO PHE ASP LEU 10.0559
77 1KPG 16A 10.1045
78 4LH7 NMN 10.2167
79 1MID LAP 10.989
80 6MVU K4V 11.4688
81 2BHW NEX 12.931
82 5THQ NDP 13.2353
83 4O4Z N2O 14.2857
84 3QKD HI0 15.4696
85 1XZ3 ICF 16.092
86 2F2G HMH 16.7421
87 1T0S BML 17.4419
88 4XCP PLM 19.4118
89 2Y69 CHD 20
90 2WTX UDP 27.5654
91 2WTX VDO 27.5654
92 5C1M OLC 32
Pocket No.: 2; Query (leader) PDB : 4F97; Ligand: VDO; Similar sites found with APoc: 47
This union binding pocket(no: 2) in the query (biounit: 4f97.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 4X7R NTO 1.21704
3 4X7R 3YW 1.21704
4 4X7R UDP 1.21704
5 1JG9 GLC 1.40845
6 6GNF ADP 1.81087
7 6GNF GLC 1.81087
8 5L6G XYP 1.81087
9 6GNF QPS 1.81087
10 2GEK GDP 1.97044
11 6E8I PTR 2.36686
12 4PQG NAG 2.61569
13 1DKU AP2 2.83912
14 3OKA GDD 2.88714
15 1TZD ADP 2.90909
16 3OKP GDD 3.04569
17 2XOC ADP 3.06513
18 4LHD GLY 3.21932
19 2IW1 U2F 3.47594
20 2XA2 UPG 3.84615
21 1RZU ADP 3.91753
22 2P9H IPT 4.08922
23 2QZS 250 4.12371
24 2QZS GLC 4.12371
25 2QZS ADP 4.12371
26 3NB0 G6P 4.22535
27 2IV3 UDP 4.38596
28 3BEO UDP 4.8
29 4NFE BEN 5.06329
30 6EJI UD2 5.36193
31 4XSU GLC 5.41237
32 4XSU UDP 5.41237
33 1EM6 NBG 5.4326
34 3X27 TRP 5.67164
35 1QM5 PLP 6.23742
36 1QM5 GLC GLC GLC PO4 SGC GLC 6.23742
37 5KOD IAC 6.23742
38 5C79 PBU 6.66667
39 3KIF GDL 7.54717
40 5ENZ UDP 8.2495
41 1JH7 UVC 10.582
42 1PVC ILE SER GLU VAL 16.1765
43 2F2G HMH 16.7421
44 5Z84 CHD 19.1781
45 1A5V Y3 20.8861
46 2WTX VDO 27.5654
47 2WTX UDP 27.5654
Pocket No.: 3; Query (leader) PDB : 4F97; Ligand: GDP; Similar sites found with APoc: 13
This union binding pocket(no: 3) in the query (biounit: 4f97.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5J6D 6H5 1.62866
2 3WR7 COA 1.76471
3 5VW2 NAP 2.21519
4 5VW2 FDA 2.21519
5 1AE1 NAP 2.9304
6 4X1T UDP 2.94118
7 4EDF UPG 4.25101
8 4AVB ACO 4.5045
9 2X7J TPP 4.82897
10 1EM6 NBG 5.4326
11 3C8Z 5CA 6.28019
12 1XV5 UDP 6.98254
13 5UWP GNP 18.8811
Pocket No.: 4; Query (leader) PDB : 4F97; Ligand: VDO; Similar sites found with APoc: 9
This union binding pocket(no: 4) in the query (biounit: 4f97.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3WIR BGC 1.40845
2 5D9X GSH 3.04348
3 5ZIC BMA Z4Y NAG 3.21932
4 4KTP BGC 4.02414
5 5AN1 GSH 5.02283
6 2YRX AMP 5.9867
7 5C9P FUC 6.82415
8 1DCP HBI 10.5769
9 4XCP PLM 19.4118
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