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 (2D)
Ligand no: 1; Ligand: 2VA; Similar ligands found: 171
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 RAB 0.513158 0.938462
11 ADN 0.513158 0.938462
12 XYA 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 NWW 0.475 0.846154
24 5CD 0.475 0.865672
25 6RE 0.471264 0.786667
26 3DH 0.470588 0.855072
27 J4G 0.470588 0.759494
28 DTA 0.46988 0.816901
29 5AL 0.46875 0.813333
30 A2P 0.466667 0.76
31 NEC 0.465909 0.880597
32 3AM 0.465116 0.783784
33 QA7 0.464646 0.828947
34 5N5 0.4625 0.909091
35 8QN 0.46 0.813333
36 A 0.45977 0.797297
37 AMP 0.45977 0.797297
38 EP4 0.457831 0.884058
39 A4D 0.45679 0.909091
40 3D1 0.45679 0.855072
41 3L1 0.45679 0.855072
42 3AD 0.45679 0.893939
43 AN2 0.456522 0.789474
44 7D3 0.455556 0.74359
45 LSS 0.455446 0.724138
46 OVE 0.454545 0.766234
47 NWQ 0.453488 0.848485
48 SA8 0.452632 0.8
49 M2T 0.452381 0.859155
50 A3P 0.450549 0.773333
51 8LQ 0.45 0.792208
52 53H 0.45 0.741176
53 5AD 0.448718 0.830769
54 SAH 0.447917 0.819444
55 SFG 0.446809 0.828571
56 9ZA 0.445545 0.794872
57 9ZD 0.445545 0.794872
58 SSA 0.444444 0.72093
59 S7M 0.444444 0.779221
60 45A 0.444444 0.8
61 8LH 0.444444 0.815789
62 ABM 0.444444 0.8
63 SAM 0.443299 0.779221
64 2A5 0.442105 0.75641
65 0UM 0.441176 0.813333
66 DSZ 0.441176 0.701149
67 52H 0.44 0.741176
68 GJV 0.43956 0.776316
69 V2G 0.438776 0.7625
70 EEM 0.438776 0.779221
71 AMP MG 0.438202 0.808219
72 ATR 0.4375 0.773333
73 NVA LMS 0.436893 0.677778
74 AHX 0.436893 0.78481
75 7D4 0.43617 0.74359
76 CA0 0.43617 0.802632
77 DAL AMP 0.435644 0.813333
78 5CA 0.435644 0.72093
79 BA3 0.434783 0.8
80 N5O 0.433333 0.869565
81 SAI 0.43299 0.808219
82 QQX 0.431818 0.717949
83 KG4 0.431579 0.802632
84 KL2 0.430233 0.746667
85 B4P 0.430108 0.8
86 AP5 0.430108 0.8
87 ADP 0.430108 0.8
88 5AS 0.430108 0.701149
89 SRP 0.43 0.792208
90 SMM 0.43 0.772152
91 A2D 0.428571 0.8
92 V3L 0.428571 0.776316
93 NSS 0.427184 0.701149
94 5FA 0.427083 0.8
95 AQP 0.427083 0.8
96 QQY 0.426966 0.727273
97 LMS 0.426966 0.702381
98 ACK 0.426966 0.767123
99 Y3J 0.426829 0.779412
100 SON 0.425532 0.769231
101 AT4 0.425532 0.769231
102 CC5 0.425 0.878788
103 TXA 0.424528 0.815789
104 ME8 0.424528 0.73494
105 NB8 0.424528 0.7625
106 SXZ 0.424528 0.826667
107 PPS 0.424242 0.702381
108 8LE 0.424242 0.828947
109 N5A 0.423913 0.84058
110 S4M 0.423913 0.75
111 PAP 0.42268 0.786667
112 SRA 0.422222 0.75641
113 M33 0.421053 0.813333
114 ADX 0.421053 0.722892
115 AU1 0.421053 0.779221
116 AP2 0.419355 0.769231
117 A12 0.419355 0.769231
118 NA7 0.419048 0.769231
119 G5A 0.418367 0.701149
120 DSH 0.417582 0.797297
121 AOC 0.417582 0.855072
122 HEJ 0.416667 0.8
123 CUU 0.416667 0.776316
124 ATP 0.416667 0.8
125 V47 0.415842 0.84058
126 KAA 0.415094 0.677778
127 GSU 0.415094 0.681818
128 GAP 0.414141 0.802632
129 AMO 0.413462 0.792208
130 PAJ 0.413462 0.844156
131 A3N 0.413043 0.869565
132 APC 0.412371 0.769231
133 NWZ 0.412371 0.797297
134 PRX 0.412371 0.779221
135 0XU 0.412371 0.802817
136 5F1 0.411765 0.760563
137 A2R 0.411765 0.789474
138 PTJ 0.411215 0.807692
139 3OD 0.411215 0.826667
140 ZAS 0.411111 0.794521
141 7MD 0.410714 0.756098
142 A7D 0.410526 0.857143
143 ADP MG 0.410526 0.797297
144 ADP BEF 0.410526 0.797297
145 DLL 0.409524 0.789474
146 62X 0.409524 0.794872
147 YSA 0.409091 0.681818
148 XAH 0.409091 0.73494
149 AGS 0.408163 0.759494
150 8X1 0.407767 0.677778
151 A22 0.407767 0.789474
152 MHZ 0.40625 0.740741
153 K15 0.40566 0.769231
154 OAD 0.40566 0.826667
155 LEU LMS 0.40566 0.732558
156 MAO 0.404255 0.740741
157 GEK 0.403846 0.786667
158 HZ2 0.403509 0.826667
159 DA 0.402174 0.717949
160 D5M 0.402174 0.717949
161 50T 0.402062 0.789474
162 ACP 0.402062 0.779221
163 LAD 0.401869 0.753086
164 ACQ 0.4 0.779221
165 3AT 0.4 0.776316
166 48N 0.4 0.78481
167 NX8 0.4 0.810811
168 4AD 0.4 0.782051
169 T99 0.4 0.769231
170 ANP 0.4 0.779221
171 TAT 0.4 0.769231
Similar Ligands (3D)
Ligand no: 1; Ligand: 2VA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 2GP 0.8788
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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