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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: 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: 95
This union binding pocket(no: 1) in the query (biounit: 1wk8.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC NBU None
2 1NNU NAD 2.06186
3 1NNU TCT 2.06186
4 3WDM ADN 2.57732
5 3LCC SAH 2.57732
6 1X1T NAD 2.57732
7 5K6A NAP 2.57732
8 3JQ7 NAP 2.57732
9 5EIN NAP 2.57732
10 4CLR NAP 2.57732
11 2P3V SRT 2.57732
12 1D1T NAD 2.57732
13 4CLO NAP 2.57732
14 2C91 NAP 2.57732
15 3JQB NAP 2.57732
16 6E8I PTR 2.95858
17 4RDN 6MD 2.99401
18 1QFY FAD 3.09278
19 1QFY NAP 3.09278
20 2O07 MTA 3.09278
21 3C3N FMN 3.09278
22 5W7M SAH 3.09278
23 1FND A2P 3.09278
24 1FND FAD 3.09278
25 2O07 SPD 3.09278
26 5XWC 8GL 3.60825
27 5XWC NAP 3.60825
28 5XWC 2IT 3.60825
29 1EU1 GLC 3.60825
30 3DRG ARG PRO PRO GLY PHE SER PRO PHE ALA 4.12371
31 2RC5 FAD 4.12371
32 1LLU NAD 4.12371
33 1X7D NAD 4.63918
34 4UYW H1S 4.63918
35 3VYW SAM 4.63918
36 4QVB F42 4.7619
37 2HNK SAH 5.02092
38 2AMT 1AA 5.03145
39 4LHD GLY 5.15464
40 5W8E ADE 5.15464
41 1EWY FAD 5.15464
42 5IKH 6BW 5.15464
43 1PVN MZP 5.15464
44 5H5J FAD 5.15464
45 3S6X SIA GAL BGC 5.6701
46 5BUK FAD 5.6701
47 3THR C2F 5.6701
48 5LOG SAH 5.6701
49 6BQ6 TER 5.6701
50 5W7K SAH 5.6701
51 5YW5 ADE 6.14525
52 5GUD NDP 6.18557
53 5GUD 2IT 6.18557
54 4W6Z 8ID 6.70103
55 1SM4 FAD 6.70103
56 1USF FMN 6.74157
57 1USF NAP 6.74157
58 3VET CP 7.2165
59 3VET TOY 7.2165
60 3VET ADP 7.2165
61 4RL4 PPV 7.2165
62 3MHP FAD 7.69231
63 1T9M FMN 7.73196
64 1SJD NPG 7.73196
65 1VBO MAN MAN MAN 7.73196
66 3BGD SAH 7.73196
67 5L3R GCP 7.73196
68 4QTB 38Z 7.73196
69 1PNF NDG NAG 8.24742
70 3PNL ADP 8.76289
71 3FPF TNA 8.76289
72 3FPF MTA 8.76289
73 1U3U NAD 8.76289
74 1U3U BNF 8.76289
75 3B6R CRN 9.27835
76 3NB0 G6P 9.27835
77 5AHO TLA 9.27835
78 5LXT GTP 9.79381
79 4HMT FMN 11.3402
80 4HMT NNV 11.3402
81 5T0K SAM 11.3402
82 4M1U MBG A2G 11.4286
83 3NZW BOC TY5 ALA RE0 ABN 13.4021
84 5KOK SAH 13.4021
85 5AHW CMP 14.966
86 5Y6Q FAD 17.9012
87 5Y6Q MCN 17.9012
88 5AGR A52 20.1031
89 5FOM A2H 21.134
90 4K47 WMP 22.3958
91 1WK9 TSB 28.0822
92 2V0C ANZ 29.8969
93 2AJH MET 34.0206
94 2WFG ZZB 38.1443
95 3SWC SAH 41.6667
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