Structure of PDB 4eg6 Chain B Binding Site BS01

Receptor Information
>4eg6 Chain B (length=515) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVF
ALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIR
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITWVSE
ENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGLPDLSVSRA
RATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLRVDESGKEVSLVDDF
NELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVAHGWWTKDR
KKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYSDKNMIARL
NGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQLIKDLPGTA
DHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPERLRTVLYIT
LEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFGAVPPGTRL
GPAVEGEVLFSKRST
Ligand information
Ligand ID0P5
InChIInChI=1S/C23H22ClN7O3/c1-33-14-6-7-18(15(24)10-14)34-22-11-19(29-23(30-22)31-9-8-25-21(32)13-31)26-12-20-27-16-4-2-3-5-17(16)28-20/h2-7,10-11H,8-9,12-13H2,1H3,(H,25,32)(H,27,28)(H,26,29,30)
InChIKeyCWWLCYZCSRQXMN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6COc1ccc(c(c1)Cl)Oc2cc(nc(n2)N3CCNC(=O)C3)NCc4[nH]c5ccccc5n4
CACTVS 3.370COc1ccc(Oc2cc(NCc3[nH]c4ccccc4n3)nc(n2)N5CCNC(=O)C5)c(Cl)c1
ACDLabs 12.01Clc5cc(OC)ccc5Oc3nc(nc(NCc2nc1ccccc1n2)c3)N4CC(=O)NCC4
FormulaC23 H22 Cl N7 O3
Name4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(2-chloro-4-methoxyphenoxy)pyrimidin-2-yl}piperazin-2-one
ChEMBL
DrugBank
ZINCZINC000095921317
PDB chain4eg6 Chain B Residue 906 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4eg6 Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection.
Resolution2.901 Å
Binding residue
(original residue number in PDB)
I248 Y250 D287 H289 G290 Y472 V473 W474 D476 Y481 I519 F522 H523
Binding residue
(residue number reindexed from 1)
I17 Y19 D56 H58 G59 Y220 V221 W222 D224 Y229 I267 F270 H271
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H256 H259 S364 D367 K554 K557
Catalytic site (residue number reindexed from 1) H25 H28 S133 D136 K302 K305
Enzyme Commision number 6.1.1.10: methionine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004825 methionine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006431 methionyl-tRNA aminoacylation

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:4eg6, PDBe:4eg6, PDBj:4eg6
PDBsum4eg6
PubMed22902861
UniProtQ38C91

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