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)...
View in 3D viewer
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: 151
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 ADN 0.513158 0.938462
11 XYA 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 DTA 0.46988 0.816901
27 5AL 0.46875 0.813333
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 3D1 0.45679 0.855072
37 A4D 0.45679 0.909091
38 3L1 0.45679 0.855072
39 3AD 0.45679 0.893939
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 9ZA 0.445545 0.794872
52 9ZD 0.445545 0.794872
53 ABM 0.444444 0.8
54 SSA 0.444444 0.72093
55 S7M 0.444444 0.779221
56 SAM 0.443299 0.779221
57 2A5 0.442105 0.75641
58 DSZ 0.441176 0.701149
59 0UM 0.441176 0.813333
60 52H 0.44 0.741176
61 GJV 0.43956 0.776316
62 EEM 0.438776 0.779221
63 ATR 0.4375 0.773333
64 AHX 0.436893 0.78481
65 NVA LMS 0.436893 0.677778
66 CA0 0.43617 0.802632
67 7D4 0.43617 0.74359
68 DAL AMP 0.435644 0.813333
69 5CA 0.435644 0.72093
70 BA3 0.434783 0.8
71 SAI 0.43299 0.808219
72 LEU LMS 0.432692 0.715909
73 QQX 0.431818 0.717949
74 5AS 0.430108 0.701149
75 ADP 0.430108 0.8
76 AP5 0.430108 0.8
77 B4P 0.430108 0.8
78 SRP 0.43 0.792208
79 SMM 0.43 0.772152
80 V3L 0.428571 0.776316
81 A2D 0.428571 0.8
82 NSS 0.427184 0.701149
83 AQP 0.427083 0.8
84 5FA 0.427083 0.8
85 QQY 0.426966 0.727273
86 LMS 0.426966 0.702381
87 ACK 0.426966 0.767123
88 Y3J 0.426829 0.779412
89 SON 0.425532 0.769231
90 AT4 0.425532 0.769231
91 CC5 0.425 0.878788
92 NB8 0.424528 0.7625
93 TXA 0.424528 0.815789
94 SXZ 0.424528 0.826667
95 ME8 0.424528 0.73494
96 PPS 0.424242 0.702381
97 S4M 0.423913 0.75
98 PAP 0.42268 0.786667
99 SRA 0.422222 0.75641
100 AU1 0.421053 0.779221
101 M33 0.421053 0.813333
102 ADX 0.421053 0.722892
103 A12 0.419355 0.769231
104 AP2 0.419355 0.769231
105 NA7 0.419048 0.769231
106 G5A 0.418367 0.701149
107 DSH 0.417582 0.797297
108 AOC 0.417582 0.855072
109 ATP 0.416667 0.8
110 HEJ 0.416667 0.8
111 GSU 0.415094 0.681818
112 KAA 0.415094 0.677778
113 GAP 0.414141 0.802632
114 AMO 0.413462 0.792208
115 PAJ 0.413462 0.844156
116 A3N 0.413043 0.869565
117 PRX 0.412371 0.779221
118 APC 0.412371 0.769231
119 0XU 0.412371 0.802817
120 A2R 0.411765 0.789474
121 5F1 0.411765 0.760563
122 PTJ 0.411215 0.807692
123 3OD 0.411215 0.826667
124 ZAS 0.411111 0.794521
125 7MD 0.410714 0.756098
126 A7D 0.410526 0.857143
127 DLL 0.409524 0.789474
128 62X 0.409524 0.794872
129 XAH 0.409091 0.73494
130 YSA 0.409091 0.681818
131 SAP 0.408163 0.759494
132 AGS 0.408163 0.759494
133 8X1 0.407767 0.677778
134 A22 0.407767 0.789474
135 MHZ 0.40625 0.740741
136 OAD 0.40566 0.826667
137 K15 0.40566 0.769231
138 MAO 0.404255 0.740741
139 GEK 0.403846 0.786667
140 D5M 0.402174 0.717949
141 DA 0.402174 0.717949
142 50T 0.402062 0.789474
143 ACP 0.402062 0.779221
144 LAD 0.401869 0.753086
145 4AD 0.4 0.782051
146 T99 0.4 0.769231
147 ACQ 0.4 0.779221
148 3AT 0.4 0.776316
149 48N 0.4 0.78481
150 TAT 0.4 0.769231
151 ANP 0.4 0.779221
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
APoc FAQ
Feedback