Structure of PDB 6i0x Chain B Binding Site BS01

Receptor Information
>6i0x Chain B (length=422) Species: 242619 (Porphyromonas gingivalis W83) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIV
ASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKV
GLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAV
QSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNNTYIDHVDCWGKY
LAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQ
PYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPW
LGTDALHCRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATIS
PVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNS
GRKETYPFIGEPDPFKFTCMNE
Ligand information
Ligand IDBFB
InChIInChI=1S/C14H20N4O2/c1-10(15)17-9-5-8-12(13(16)19)18-14(20)11-6-3-2-4-7-11/h2-4,6-7,12H,5,8-9H2,1H3,(H2,15,17)(H2,16,19)(H,18,20)/t12-/m0/s1
InChIKeyLWFFSSMDFWZNNW-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=N)NCCC[CH](NC(=O)c1ccccc1)C(N)=O
ACDLabs 10.04O=C(NC(C(=O)N)CCCNC(=[N@H])C)c1ccccc1
OpenEye OEToolkits 1.5.0[H]N=C(C)NCCCC(C(=O)N)NC(=O)c1ccccc1
OpenEye OEToolkits 1.5.0[H]/N=C(/C)\NCCC[C@@H](C(=O)N)NC(=O)c1ccccc1
CACTVS 3.341CC(=N)NCCC[C@H](NC(=O)c1ccccc1)C(N)=O
FormulaC14 H20 N4 O2
NameN-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE;
(S)-N-ALPHA-BENZOYL-N5-(2-FLUORO-1-IMINOETHYL)-L-ORNITHINE AMIDE
ChEMBL
DrugBankDB07449
ZINCZINC000016051936
PDB chain6i0x Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6i0x Structure, function, and inhibition of a genomic/clinical variant of Porphyromonas gingivalis peptidylarginine deiminase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		W127 D130 R152 R154 Y233 I234 H236 D238 T346 C351
Binding residue
(residue number reindexed from 1)		W84 D87 R109 R111 Y190 I191 H193 D195 T303 C308
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.3.-
Gene Ontology
Molecular Function
GO:0004668 protein-arginine deiminase activity
Biological Process
GO:0009446 putrescine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6i0x, PDBe:6i0x, PDBj:6i0x
PDBsum6i0x
PubMed30638292
UniProtQ9RQJ2|PAD_PORGI Peptidylarginine deiminase (Gene Name=PG_1424)

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