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: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 2VA 1 1
2 SO8 0.828947 0.955224
3 VRT 0.7375 0.9
4 NVA 2AD 0.725 0.887324
5 A3T 0.619048 0.969231
6 A3S 0.55814 0.925373
7 VMS 0.531915 0.75
8 54H 0.531915 0.75
9 A3G 0.517647 0.911765
10 XYA 0.513158 0.938462
11 ADN 0.513158 0.938462
12 RAB 0.513158 0.938462
13 7D7 0.5 0.823529
14 D3Y 0.494845 0.898551
15 7D5 0.493976 0.74026
16 2AM 0.488095 0.797297
17 3NZ 0.485149 0.887324
18 MTA 0.481928 0.855072
19 TSB 0.479592 0.738095
20 A5A 0.479167 0.72619
21 5X8 0.478261 0.842857
22 J7C 0.477273 0.797297
23 5CD 0.475 0.865672
24 6RE 0.471264 0.786667
25 3DH 0.470588 0.855072
26 J4G 0.470588 0.759494
27 DTA 0.46988 0.816901
28 5AL 0.46875 0.813333
29 A2P 0.466667 0.76
30 NEC 0.465909 0.880597
31 3AM 0.465116 0.783784
32 5N5 0.4625 0.909091
33 8QN 0.46 0.813333
34 AMP 0.45977 0.797297
35 A 0.45977 0.797297
36 EP4 0.457831 0.884058
37 3D1 0.45679 0.855072
38 3AD 0.45679 0.893939
39 3L1 0.45679 0.855072
40 A4D 0.45679 0.909091
41 AN2 0.456522 0.789474
42 7D3 0.455556 0.74359
43 LSS 0.455446 0.724138
44 OVE 0.454545 0.766234
45 SA8 0.452632 0.8
46 M2T 0.452381 0.859155
47 A3P 0.450549 0.773333
48 8LQ 0.45 0.792208
49 53H 0.45 0.741176
50 5AD 0.448718 0.830769
51 SAH 0.447917 0.819444
52 SFG 0.446809 0.828571
53 9ZA 0.445545 0.794872
54 9ZD 0.445545 0.794872
55 S7M 0.444444 0.779221
56 ABM 0.444444 0.8
57 45A 0.444444 0.8
58 SSA 0.444444 0.72093
59 8LH 0.444444 0.815789
60 SAM 0.443299 0.779221
61 2A5 0.442105 0.75641
62 DSZ 0.441176 0.701149
63 0UM 0.441176 0.813333
64 52H 0.44 0.741176
65 GJV 0.43956 0.776316
66 EEM 0.438776 0.779221
67 ATR 0.4375 0.773333
68 NVA LMS 0.436893 0.677778
69 AHX 0.436893 0.78481
70 CA0 0.43617 0.802632
71 7D4 0.43617 0.74359
72 DAL AMP 0.435644 0.813333
73 5CA 0.435644 0.72093
74 BA3 0.434783 0.8
75 N5O 0.433333 0.869565
76 SAI 0.43299 0.808219
77 LEU LMS 0.432692 0.715909
78 QQX 0.431818 0.717949
79 KG4 0.431579 0.802632
80 B4P 0.430108 0.8
81 5AS 0.430108 0.701149
82 AP5 0.430108 0.8
83 ADP 0.430108 0.8
84 SMM 0.43 0.772152
85 SRP 0.43 0.792208
86 V3L 0.428571 0.776316
87 A2D 0.428571 0.8
88 NSS 0.427184 0.701149
89 AQP 0.427083 0.8
90 5FA 0.427083 0.8
91 QQY 0.426966 0.727273
92 LMS 0.426966 0.702381
93 ACK 0.426966 0.767123
94 Y3J 0.426829 0.779412
95 AT4 0.425532 0.769231
96 SON 0.425532 0.769231
97 CC5 0.425 0.878788
98 SXZ 0.424528 0.826667
99 TXA 0.424528 0.815789
100 NB8 0.424528 0.7625
101 ME8 0.424528 0.73494
102 8LE 0.424242 0.828947
103 PPS 0.424242 0.702381
104 N5A 0.423913 0.84058
105 S4M 0.423913 0.75
106 PAP 0.42268 0.786667
107 SRA 0.422222 0.75641
108 M33 0.421053 0.813333
109 AU1 0.421053 0.779221
110 ADX 0.421053 0.722892
111 AP2 0.419355 0.769231
112 A12 0.419355 0.769231
113 NA7 0.419048 0.769231
114 G5A 0.418367 0.701149
115 AOC 0.417582 0.855072
116 DSH 0.417582 0.797297
117 HEJ 0.416667 0.8
118 ATP 0.416667 0.8
119 KAA 0.415094 0.677778
120 GSU 0.415094 0.681818
121 GAP 0.414141 0.802632
122 AMO 0.413462 0.792208
123 PAJ 0.413462 0.844156
124 A3N 0.413043 0.869565
125 PRX 0.412371 0.779221
126 APC 0.412371 0.769231
127 0XU 0.412371 0.802817
128 5F1 0.411765 0.760563
129 A2R 0.411765 0.789474
130 PTJ 0.411215 0.807692
131 3OD 0.411215 0.826667
132 ZAS 0.411111 0.794521
133 7MD 0.410714 0.756098
134 A7D 0.410526 0.857143
135 ADP MG 0.410526 0.797297
136 62X 0.409524 0.794872
137 DLL 0.409524 0.789474
138 XAH 0.409091 0.73494
139 YSA 0.409091 0.681818
140 AGS 0.408163 0.759494
141 SAP 0.408163 0.759494
142 A22 0.407767 0.789474
143 8X1 0.407767 0.677778
144 MHZ 0.40625 0.740741
145 K15 0.40566 0.769231
146 OAD 0.40566 0.826667
147 MAO 0.404255 0.740741
148 GEK 0.403846 0.786667
149 HZ2 0.403509 0.826667
150 D5M 0.402174 0.717949
151 DA 0.402174 0.717949
152 50T 0.402062 0.789474
153 ACP 0.402062 0.779221
154 LAD 0.401869 0.753086
155 T99 0.4 0.769231
156 ACQ 0.4 0.779221
157 4AD 0.4 0.782051
158 ANP 0.4 0.779221
159 TAT 0.4 0.769231
160 48N 0.4 0.78481
161 3AT 0.4 0.776316
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1WK8; Ligand: VMS; 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: 1wk8.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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