Structure of PDB 4q3b Chain D Binding Site BS03

Receptor Information
>4q3b Chain D (length=260) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVG
IVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEI
ILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGL
GKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSI
IFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGI
GTASMLYSVL
Ligand information
Ligand ID2YF
InChIInChI=1S/C12H21N3O3/c13-9(12(17)18)5-1-3-8-15-11(16)10-6-2-4-7-14-10/h7,9-10H,1-6,8,13H2,(H,15,16)(H,17,18)/t9-,10+/m0/s1
InChIKeyKRPZACZJBBRBIT-VHSXEESVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1CC=NC(C1)C(=O)NCCCCC(C(=O)O)N
ACDLabs 12.01O=C(NCCCCC(C(=O)O)N)C1N=CCCC1
OpenEye OEToolkits 1.7.6C1CC=N[C@H](C1)C(=O)NCCCC[C@@H](C(=O)O)N
CACTVS 3.385N[C@@H](CCCCNC(=O)[C@H]1CCCC=N1)C(O)=O
CACTVS 3.385N[CH](CCCCNC(=O)[CH]1CCCC=N1)C(O)=O
FormulaC12 H21 N3 O3
NameN~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine
ChEMBL
DrugBank
ZINCZINC000098208351
PDB chain4q3b Chain D Residue 904 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4q3b The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).
Resolution1.9 Å
Binding residue
(original residue number in PDB)		L3 L4 P52 V53 I59 I60 F63 A103
Binding residue
(residue number reindexed from 1)		L4 L5 P53 V54 I60 I61 F64 A104
Annotation score3
Enzymatic activity
Enzyme Commision number 1.4.1.-
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
Biological Process
GO:0008652 amino acid biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:4q3b, PDBe:4q3b, PDBj:4q3b
PDBsum4q3b
PubMed24916332
UniProtQ46E80|PYLD_METBF Pyrrolysine synthase (Gene Name=pylD)

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