Structure of PDB 4h2v Chain A Binding Site BS04

Receptor Information
>4h2v Chain A (length=295) Species: 224911 (Bradyrhizobium diazoefficiens USDA 110) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRF
PPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTT
SLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLD
RLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPF
FGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGI
QDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL
Ligand information
Ligand IDH2V
InChIInChI=1S/C13H26N3O8PS/c1-13(2,8-24-25(21,22)23)11(19)12(20)16-4-3-9(17)15-5-6-26-10(18)7-14/h11,19H,3-8,14H2,1-2H3,(H,15,17)(H,16,20)(H2,21,22,23)/t11-/m1/s1
InChIKeyCGYKHWUDQZHKBD-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(COP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CN)O
CACTVS 3.370CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CN
CACTVS 3.370CC(C)(CO[P](O)(O)=O)[C@H](O)C(=O)NCCC(=O)NCCSC(=O)CN
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)O)CN
FormulaC13 H26 N3 O8 P S
NameS-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] aminoethanethioate;
S-glycyl-4'-phosphopantetheine
ChEMBL
DrugBank
ZINCZINC000098208980
PDB chain4h2v Chain C Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4h2v Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
Y132 F217 K225 Q229 N255 H257 C279
Binding residue
(residue number reindexed from 1)
Y115 F200 K208 Q212 N238 H240 C262
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C131 R159 E161 R168 E176 K235 A250 S253 C279 R286
Catalytic site (residue number reindexed from 1) C114 R142 E144 R151 E159 K218 A233 S236 C262 R269
Enzyme Commision number 6.2.1.n2: amino acid--[acyl-carrier-protein] ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4h2v, PDBe:4h2v, PDBj:4h2v
PDBsum4h2v
PubMed23541895
UniProtQ89VT8|AACL1_BRADU Amino acid--[acyl-carrier-protein] ligase 1 (Gene Name=bll0957)

[Back to BioLiP]