Structure of PDB 4q39 Chain B Binding Site BS03

Receptor Information
>4q39 Chain B (length=259) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGI
VPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEII
LMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLG
KVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSII
FEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIG
TASMLYSVL
Ligand information
Ligand IDPYL
InChIInChI=1S/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9+,10-/m1/s1
InChIKeyZFOMKMMPBOQKMC-KXUCPTDWSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCCCCC(C(=O)O)N)C1N=CCC1C
OpenEye OEToolkits 1.7.6CC1CC=NC1C(=O)NCCCCC(C(=O)O)N
CACTVS 3.385C[CH]1CC=N[CH]1C(=O)NCCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.7.6C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@@H](C(=O)O)N
CACTVS 3.385C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@H](N)C(O)=O
FormulaC12 H21 N3 O3
NamePYRROLYSINE
ChEMBL
DrugBank
ZINC
PDB chain4q39 Chain B Residue 904 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4q39 The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).
Resolution2.2 Å
Binding residue
(original residue number in PDB)		L3 L4 V53 G58 I59 I60 F63 F108
Binding residue
(residue number reindexed from 1)		L3 L4 V53 G58 I59 I60 F63 F108
Annotation score5
Enzymatic activity
Enzyme Commision number 1.4.1.-
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
Biological Process
GO:0008652 amino acid biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4q39, PDBe:4q39, PDBj:4q39
PDBsum4q39
PubMed24916332
UniProtQ46E80|PYLD_METBF Pyrrolysine synthase (Gene Name=pylD)

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