Receptor
PDB id Resolution Class Description Source Keywords
1WNZ 1.7 Å EC: 6.1.1.5 ISOLEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEXED WITH THE POST-TRANSFER EDITING SUBSTRATE ANALOGUE, VAL-2AA THERMUS THERMOPHILUS LIGASE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY THE EDITING DOMAIN OF ISOLEUCYL-TRNA SYNTHETASE J.MOL.BIOL. V. 359 901 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2VA A:901;
Valid;
none;
submit data
365.388 C15 H23 N7 O4 CC(C)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1WK8 1.7 Å EC: 6.1.1.5 ISOLEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEXED WITH THE PRE-TRANSFER EDITING SUBSTRATE ANALOGUE, VAL-AMS THERMUS THERMOPHILUS EDITING CP1 ISOLEUCYL-TRNA SYNTHETASE FIDELITY THERMUS THERMOPHILUS TRANSLATION AMINO ACID STRUCTURAL GENOMICSRIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES LIGASE
Ref.: STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY THE EDITING DOMAIN OF ISOLEUCYL-TRNA SYNTHETASE J.MOL.BIOL. V. 359 901 2006
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1WK8 - VMS C15 H23 N7 O7 S CC(C)[C@@H....
2 1WNZ - 2VA C15 H23 N7 O4 CC(C)[C@@H....
3 1UE0 - VAL C5 H11 N O2 CC(C)[C@@H....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1WK8 - VMS C15 H23 N7 O7 S CC(C)[C@@H....
2 1WNZ - 2VA C15 H23 N7 O4 CC(C)[C@@H....
3 1UE0 - VAL C5 H11 N O2 CC(C)[C@@H....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1WK8 - VMS C15 H23 N7 O7 S CC(C)[C@@H....
2 1WNZ - 2VA C15 H23 N7 O4 CC(C)[C@@H....
3 1UE0 - VAL C5 H11 N O2 CC(C)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2VA; Similar ligands found: 148
No: Ligand ECFP6 Tc MDL keys Tc
1 2VA 1 1
2 SO8 0.828947 0.955224
3 VRT 0.7375 0.9
4 A3T 0.619048 0.969231
5 A3S 0.55814 0.925373
6 VMS 0.531915 0.75
7 54H 0.531915 0.75
8 A3G 0.517647 0.911765
9 XYA 0.513158 0.938462
10 ADN 0.513158 0.938462
11 RAB 0.513158 0.938462
12 7D7 0.5 0.823529
13 D3Y 0.494845 0.898551
14 7D5 0.493976 0.74026
15 2AM 0.488095 0.797297
16 3NZ 0.485149 0.887324
17 MTA 0.481928 0.855072
18 TSB 0.479592 0.738095
19 A5A 0.479167 0.72619
20 5X8 0.478261 0.842857
21 J7C 0.477273 0.797297
22 5CD 0.475 0.865672
23 6RE 0.471264 0.786667
24 3DH 0.470588 0.855072
25 DTA 0.46988 0.816901
26 5AL 0.46875 0.813333
27 NVA 2AD 0.468085 0.871429
28 A2P 0.466667 0.76
29 NEC 0.465909 0.880597
30 3AM 0.465116 0.783784
31 5N5 0.4625 0.909091
32 8QN 0.46 0.813333
33 A 0.45977 0.797297
34 AMP 0.45977 0.797297
35 EP4 0.457831 0.884058
36 3AD 0.45679 0.893939
37 3D1 0.45679 0.855072
38 3L1 0.45679 0.855072
39 A4D 0.45679 0.909091
40 AN2 0.456522 0.789474
41 7D3 0.455556 0.74359
42 LSS 0.455446 0.724138
43 OVE 0.454545 0.766234
44 SA8 0.452632 0.8
45 M2T 0.452381 0.859155
46 A3P 0.450549 0.773333
47 53H 0.45 0.741176
48 5AD 0.448718 0.830769
49 SAH 0.447917 0.819444
50 SFG 0.446809 0.828571
51 SSA 0.444444 0.72093
52 S7M 0.444444 0.779221
53 ABM 0.444444 0.8
54 SAM 0.443299 0.779221
55 2A5 0.442105 0.75641
56 DSZ 0.441176 0.701149
57 0UM 0.441176 0.813333
58 52H 0.44 0.741176
59 GJV 0.43956 0.776316
60 EEM 0.438776 0.779221
61 ATR 0.4375 0.773333
62 AHX 0.436893 0.78481
63 CA0 0.43617 0.802632
64 7D4 0.43617 0.74359
65 5CA 0.435644 0.72093
66 DAL AMP 0.435644 0.813333
67 BA3 0.434783 0.8
68 AMP MG 0.433333 0.776316
69 SAI 0.43299 0.808219
70 LEU LMS 0.432692 0.724138
71 QQX 0.431818 0.717949
72 ADP 0.430108 0.8
73 B4P 0.430108 0.8
74 AP5 0.430108 0.8
75 5AS 0.430108 0.701149
76 SRP 0.43 0.792208
77 SMM 0.43 0.772152
78 A2D 0.428571 0.8
79 V3L 0.428571 0.776316
80 NSS 0.427184 0.701149
81 AQP 0.427083 0.8
82 5FA 0.427083 0.8
83 ACK 0.426966 0.767123
84 QQY 0.426966 0.727273
85 Y3J 0.426829 0.779412
86 SON 0.425532 0.769231
87 CC5 0.425 0.878788
88 ME8 0.424528 0.73494
89 NB8 0.424528 0.7625
90 SXZ 0.424528 0.826667
91 TXA 0.424528 0.815789
92 PPS 0.424242 0.702381
93 S4M 0.423913 0.75
94 NVA LMS 0.423077 0.685393
95 PAP 0.42268 0.786667
96 SRA 0.422222 0.75641
97 ADX 0.421053 0.722892
98 AU1 0.421053 0.779221
99 M33 0.421053 0.813333
100 A12 0.419355 0.769231
101 AP2 0.419355 0.769231
102 NA7 0.419048 0.769231
103 G5A 0.418367 0.701149
104 DSH 0.417582 0.797297
105 AOC 0.417582 0.855072
106 ATP 0.416667 0.8
107 GSU 0.415094 0.681818
108 KAA 0.415094 0.677778
109 GAP 0.414141 0.802632
110 AMO 0.413462 0.792208
111 PAJ 0.413462 0.844156
112 A3N 0.413043 0.869565
113 0XU 0.412371 0.802817
114 APC 0.412371 0.769231
115 PRX 0.412371 0.779221
116 A2R 0.411765 0.789474
117 5F1 0.411765 0.760563
118 PTJ 0.411215 0.807692
119 3OD 0.411215 0.826667
120 ZAS 0.411111 0.794521
121 7MD 0.410714 0.756098
122 A7D 0.410526 0.857143
123 62X 0.409524 0.794872
124 DLL 0.409524 0.789474
125 XAH 0.409091 0.73494
126 YSA 0.409091 0.681818
127 SAP 0.408163 0.759494
128 AGS 0.408163 0.759494
129 A22 0.407767 0.789474
130 ADP MG 0.40625 0.766234
131 MHZ 0.40625 0.740741
132 OAD 0.40566 0.826667
133 K15 0.40566 0.769231
134 MAO 0.404255 0.740741
135 GEK 0.403846 0.786667
136 DA 0.402174 0.717949
137 D5M 0.402174 0.717949
138 BEF ADP 0.402062 0.746835
139 50T 0.402062 0.789474
140 ADP BEF 0.402062 0.746835
141 ACP 0.402062 0.779221
142 LAD 0.401869 0.753086
143 3AT 0.4 0.776316
144 ACQ 0.4 0.779221
145 ANP 0.4 0.779221
146 4AD 0.4 0.782051
147 TAT 0.4 0.769231
148 48N 0.4 0.78481
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1WK8; Ligand: VMS; Similar sites found: 25
This union binding pocket(no: 1) in the query (biounit: 1wk8.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BOS GLA GAL GLC NBU 0.007139 0.4212 None
2 3IT7 TLA 0.0156 0.40534 2.74725
3 4RDN 6MD 0.01543 0.40387 2.99401
4 1QFY FAD 0.02904 0.40904 3.09278
5 1QFY NAP 0.02904 0.40904 3.09278
6 1EU1 GLC 0.001868 0.40493 3.60825
7 4UYW H1S 0.006999 0.4048 4.63918
8 2AMT 1AA 0.02019 0.40647 5.03145
9 5H5J FAD 0.01606 0.4019 5.15464
10 3S6X SIA GAL BGC 0.0007307 0.46956 5.6701
11 4W6Z 8ID 0.04258 0.40037 6.70103
12 4RL4 PPV 0.003023 0.44549 7.2165
13 3MHP FAD 0.01695 0.40076 7.69231
14 1VBO MAN MAN MAN 0.01211 0.40456 7.73196
15 3PNL ADP 0.01597 0.4071 8.76289
16 3B6R CRN 0.02004 0.41663 9.27835
17 5AHO TLA 0.01899 0.40901 9.27835
18 4M1U MBG A2G 0.0229 0.40087 11.4286
19 5AHW CMP 0.01455 0.40015 14.966
20 5AGR A52 0.0000003541 0.56766 20.1031
21 4K47 WMP 0.000004518 0.5641 22.3958
22 1WK9 TSB 0.000008027 0.54904 28.0822
23 2V0C ANZ 0.00000006125 0.58428 29.8969
24 2AJH MET 0.0000009142 0.61442 34.0206
25 2WFG ZZB 0.000002171 0.58845 38.1443
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