Structure of PDB 4q3d Chain D Binding Site BS03

Receptor Information
>4q3d Chain D (length=256) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPV
TSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMA
DDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVG
FPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEA
TPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTAS
MLYSVL
Ligand information
Ligand ID2YH
InChIInChI=1S/C10H22N4O3/c11-5-1-3-7(12)9(15)14-6-2-4-8(13)10(16)17/h7-8H,1-6,11-13H2,(H,14,15)(H,16,17)/t7-,8+/m1/s1
InChIKeyMCMLHDBHZRLOED-SFYZADRCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(N)CCCNC(=O)C(N)CCCN
CACTVS 3.385NCCC[C@@H](N)C(=O)NCCC[C@H](N)C(O)=O
CACTVS 3.385NCCC[CH](N)C(=O)NCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.7.6C(C[C@H](C(=O)NCCC[C@@H](C(=O)O)N)N)CN
OpenEye OEToolkits 1.7.6C(CC(C(=O)NCCCC(C(=O)O)N)N)CN
FormulaC10 H22 N4 O3
NameN~5~-D-ornithyl-L-ornithine
ChEMBL
DrugBank
ZINCZINC000098208352
PDB chain4q3d Chain D Residue 904 [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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PDB4q3d 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)		P52 V53 G58 I59 I60 F63 A103 D104 D105 R106 Q122
Binding residue
(residue number reindexed from 1)		P49 V50 G55 I56 I57 F60 A100 D101 D102 R103 Q119
Annotation score2
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:4q3d, PDBe:4q3d, PDBj:4q3d
PDBsum4q3d
PubMed24916332
UniProtQ46E80|PYLD_METBF Pyrrolysine synthase (Gene Name=pylD)

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