Structure of PDB 7d56 Chain B Binding Site BS01

Receptor Information
>7d56 Chain B (length=635) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSLQRIVRVSLEHPTSAVCVAGVETLVDIYGSVPEGTEMFEVYGTPGVDI
YISPNMERGRERADTRRWRFDATLEIIVVMNSPSNDLNDSHVQISYHSSH
EPLPLAYAVLYLTCVDISLDCDLNVDKRQWVWGPSGYGGILLVNCDRDDV
QDNCDQHVHCLQDLEDMSVMVLRTQGPAALFDDHKLVLHTSSYDAKRAQV
FHICGPEDVCEAYRHVLGQDKVSYEVPRLHGDEERFFVEGLSFPDAGFTG
LISFHVTLLDDSASPIFTDTVVFRVAPWIMTPSTLPPLEVYVCRVRNNTC
FVDAVAELARKAGCKLTICPQARWIQDEMELGYVQAPHKTLPVVFDSPRN
GELQDFPYKRILGPDFGYVTREPRSVSGLDSFGNLEVSPPVVANGKEYPL
GRILIGGNLPGSRRVTQVVRDFLHAQKVQPPVELFVDWLAVGHVDEFLSF
VPAPDGKGFRMLLASPGACFKLFQEKQKCGHGRALLFQGVVDDVKTISIN
QVLSNKDLINYNKFVQSCIDWNREVLKRELGLAECDIIDIPQLFKTERKK
ATAFFPDLVNMLVLGKHLGIPKPFGPIINGCCCLEEKVRSLLEPLGLHCT
FIDDFTPYHMLHGEVHCGTNVCRKPFSFKWWNMVP
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 chain7d56 Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7d56 Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design.
Resolution3.175 Å
Binding residue
(original residue number in PDB)		W347 D350 H470 L640 H641 C646
Binding residue
(residue number reindexed from 1)		W324 D327 H443 L611 H612 C617
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.3.15: protein-arginine deiminase.
Gene Ontology
Molecular Function
GO:0004668 protein-arginine deiminase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:7d56, PDBe:7d56, PDBj:7d56
PDBsum7d56
PubMed33971157
UniProtQ9ULW8|PADI3_HUMAN Protein-arginine deiminase type-3 (Gene Name=PADI3)

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