Structure of PDB 3t0t Chain B Binding Site BS01

Receptor Information
>3t0t Chain B (length=583) Species: 282458 (Staphylococcus aureus subsp. aureus MRSA252) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRKTKIVCTIGPASESEEMIEKLINAGMNVARLNFSHGSHEEHKGRIDTI
RKVAKRLDKIVAILLDTKGPEIRTHNMKDGIIELERGNEVIVSMNEVEGT
PEKFSVTYENLINDVQVGSYILLDDGLIELQVKDIDHAKKEVKCDILNSG
ELKNKKGVNLPGVRVSLPGITEKDAEDIRFGIKENVDFIAASFVRRPSDV
LEIREILEEQKANISVFPKIENQEGIDNIEEILEVSDGLMVARGDMGVEI
PPEKVPMVQKDLIRQCNKLGKPVITATQMLDSMQRNPRATRAEASDVANA
IYDGTDAVMLSGETAAGLYPEEAVKTMRNIAVSAEAAQDYKKLLSDRTKL
VETSLVNAIGISVAHTALNLNVKAIVAATESGSTARTISKYRPHSDIIAV
TPSEETARQCSIVWGVQPVVKKGRKSTDALLNNAVATAVETGRVTNGDLI
IITAGVPTGETGTTNMMKIHLVGDEIANGQGIGRGSVVGTTLVAETVKDL
EGKDLSDKVIVTNSIDETFVPYVEKALGLITEENGITSPSAIVGLEKGIP
TVVGVEKAVKNISNNVLVTIDAAQGKIFEGYAN
Ligand information
Ligand IDI30
InChIInChI=1S/C16H13BrN4O2/c1-9(15-18-12-4-2-3-5-13(12)19-15)20-21-16(23)11-8-10(17)6-7-14(11)22/h2-8,22H,1H3,(H,18,19)(H,21,23)/b20-9+
InChIKeyQYPYMNJXDLGLRD-AWQFTUOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2C/C(=N\NC(=O)c1cc(ccc1O)Br)/c2[nH]c3ccccc3n2
OpenEye OEToolkits 1.7.2CC(=NNC(=O)c1cc(ccc1O)Br)c2[nH]c3ccccc3n2
CACTVS 3.370CC(=NNC(=O)c1cc(Br)ccc1O)c2[nH]c3ccccc3n2
ACDLabs 12.01Brc1cc(c(O)cc1)C(=O)N\N=C(\c3nc2ccccc2n3)C
CACTVS 3.370C\C(=N/NC(=O)c1cc(Br)ccc1O)c2[nH]c3ccccc3n2
FormulaC16 H13 Br N4 O2
NameN'-[(1E)-1-(1H-benzimidazol-2-yl)ethylidene]-5-bromo-2-hydroxybenzohydrazide
ChEMBLCHEMBL2206164
DrugBank
ZINCZINC000095101421
PDB chain3t0t Chain A Residue 586 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3t0t Cheminformatics-driven discovery of selective, nanomolar inhibitors for staphylococcal pyruvate kinase.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		I361 S362 H365 T366 N369 L370
Binding residue
(residue number reindexed from 1)		I361 S362 H365 T366 N369 L370
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.04,IC50=91nM
BindingDB: IC50=91nM
Enzymatic activity
Catalytic site (original residue number in PDB) R32 R73 K219 T277
Catalytic site (residue number reindexed from 1) R32 R73 K219 T277
Enzyme Commision number 2.7.1.40: pyruvate kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004743 pyruvate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0030955 potassium ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006096 glycolytic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3t0t, PDBe:3t0t, PDBj:3t0t
PDBsum3t0t
PubMed22066782
UniProtQ6GG09|KPYK_STAAR Pyruvate kinase (Gene Name=pyk)

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