Structure of PDB 2y60 Chain A Binding Site BS01

Receptor Information
>2y60 Chain A (length=329) Species: 227321 (Aspergillus nidulans FGSC A4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQ
RLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVES
FCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGL
SSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKT
AADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLIN
CGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREP
NGKSDREPLSYGDYLQNGLVSLINKNGQT
Ligand information
Ligand IDM8F
InChIInChI=1S/C14H25N3O6S2/c1-25-6-5-9(14(22)23)17-12(19)10(7-24)16-11(18)4-2-3-8(15)13(20)21/h8-10,24H,2-7,15H2,1H3,(H,16,18)(H,17,19)(H,20,21)(H,22,23)/t8-,9+,10-/m0/s1
InChIKeyIHAISQWKLZGNMD-AEJSXWLSSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CSCC[CH](NC(=O)[CH](CS)NC(=O)CCC[CH](N)C(O)=O)C(O)=O
CACTVS 3.352CSCC[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(O)=O)C(O)=O
ACDLabs 12.01O=C(NC(C(=O)O)CCSC)C(NC(=O)CCCC(C(=O)O)N)CS
OpenEye OEToolkits 1.6.1CSCC[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](C(=O)O)N
OpenEye OEToolkits 1.6.1CSCCC(C(=O)O)NC(=O)C(CS)NC(=O)CCCC(C(=O)O)N
FormulaC14 H25 N3 O6 S2
NameN-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-methionine;
L-D-(A-aminoadipoyl)-L-cysteinyl-D-methionine
ChEMBL
DrugBank
ZINCZINC000098209158
PDB chain2y60 Chain A Residue 1332 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y60 The Crystal Structure of Isopenicillin N Synthase with Delta((L)-Alpha-Aminoadipoyl)-(L)-Cysteinyl-(D)-Methionine Reveals Thioether Coordination to Iron.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		R87 C104 S183 I187 Y189 H214 D216 H270 S281 F285 L324
Binding residue
(residue number reindexed from 1)		R85 C102 S181 I185 Y187 H212 D214 H268 S279 F283 L322
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) L186 F211 H214 D216 H270
Catalytic site (residue number reindexed from 1) L184 F209 H212 D214 H268
Enzyme Commision number 1.21.3.1: isopenicillin-N synthase.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0016216 isopenicillin-N synthase activity
GO:0016491 oxidoreductase activity
GO:0031418 L-ascorbic acid binding
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process
GO:0017000 antibiotic biosynthetic process
GO:0042318 penicillin biosynthetic process
GO:0044283 small molecule biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2y60, PDBe:2y60, PDBj:2y60
PDBsum2y60
PubMed22001738
UniProtP05326|IPNA_EMENI Isopenicillin N synthase (Gene Name=ipnA)

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