Structure of PDB 3t07 Chain B Binding Site BS01

Receptor Information
>3t07 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 ID09C
InChIInChI=1S/C20H16Br2N4O/c21-10-1-3-12-14(7-23-16(12)5-10)18-9-25-20(27)19(26-18)15-8-24-17-6-11(22)2-4-13(15)17/h1-8,18-19,23-24,26H,9H2,(H,25,27)/t18-,19-/m0/s1
InChIKeyOXVVLWOQGFZGEO-OALUTQOASA-N
SMILES
SoftwareSMILES
CACTVS 3.370Brc1ccc2c([nH]cc2[C@@H]3CNC(=O)[C@@H](N3)c4c[nH]c5cc(Br)ccc45)c1
CACTVS 3.370Brc1ccc2c([nH]cc2[CH]3CNC(=O)[CH](N3)c4c[nH]c5cc(Br)ccc45)c1
ACDLabs 12.01Brc1cc2c(cc1)c(cn2)C5C(=O)NCC(c3cnc4cc(Br)ccc34)N5
OpenEye OEToolkits 1.7.2c1cc2c(cc1Br)[nH]cc2[C@H]3C(=O)NCC(N3)c4c[nH]c5c4ccc(c5)Br
OpenEye OEToolkits 1.7.2c1cc2c(cc1Br)[nH]cc2C3CNC(=O)C(N3)c4c[nH]c5c4ccc(c5)Br
FormulaC20 H16 Br2 N4 O
Name(3S,5R)-3,5-bis(6-bromo-1H-indol-3-yl)piperazin-2-one;
cis-3,4-dihydrohamacanthin B
ChEMBLCHEMBL541209
DrugBank
ZINCZINC000015266927
PDB chain3t07 Chain B Residue 586 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t07 Methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase as a target for bis-indole alkaloids with antibacterial activities.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		A358 I361 H365 N369 L370
Binding residue
(residue number reindexed from 1)		A358 I361 H365 N369 L370
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.80,IC50=16nM
BindingDB: IC50=16nM
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:3t07, PDBe:3t07, PDBj:3t07
PDBsum3t07
PubMed22030393
UniProtQ6GG09|KPYK_STAAR Pyruvate kinase (Gene Name=pyk)

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