Structure of PDB 4x8c Chain A Binding Site BS03

Receptor Information
>4x8c Chain A (length=554) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QGTLIRVTPEQPTHAVCVLGTLTQLDICSSACTSFSINASPGVVVDIWPL
EVTLTMKVASGSTGDQKVQISYYPVKALLYLTGVEISLCADITRTGKVKP
KDQRTWTWGPCGQGAILLVNCDSEDLQDMSLMTLSTKTPKDFFTNHTLVL
HVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYV
EALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPN
TQPPQEVYACNEDFLKSVTTLAMKAKCKLTICDEMEIGYIQAPHKTLPVV
FDSFGYSGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQ
ALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPR
SCYKLFQEQQNEGHGEALLFEKQQKIKNILSNKTLREHNSFVERCIDWNR
ELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPK
PFCCLEEKVCSLLEPLGLQCTFINDFFTYHIGEVHAGTNVRRKPFSFKWW
NMVP
Ligand information
Ligand ID3YZ
InChIInChI=1S/C26H30N6O3/c1-30-23-19(10-17(12-22(23)35-2)26(34)31-9-7-21(33)18(27)14-31)29-25(30)20-11-16-4-3-8-28-24(16)32(20)13-15-5-6-15/h3-4,8,10-12,15,18,21,33H,5-7,9,13-14,27H2,1-2H3/t18-,21+/m0/s1
InChIKeySHBUAYSOPVZNDD-GHTZIAJQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cn1c2c(cc(cc2OC)C(=O)N3CCC(C(C3)N)O)nc1c4cc5cccnc5n4CC6CC6
CACTVS 3.385COc1cc(cc2nc(n(C)c12)c3cc4cccnc4n3CC5CC5)C(=O)N6CC[C@@H](O)[C@@H](N)C6
ACDLabs 12.01O=C(c5cc4nc(c2cc1cccnc1n2CC3CC3)n(c4c(OC)c5)C)N6CCC(O)C(N)C6
OpenEye OEToolkits 1.9.2Cn1c2c(cc(cc2OC)C(=O)N3CC[C@H]([C@H](C3)N)O)nc1c4cc5cccnc5n4CC6CC6
CACTVS 3.385COc1cc(cc2nc(n(C)c12)c3cc4cccnc4n3CC5CC5)C(=O)N6CC[CH](O)[CH](N)C6
FormulaC26 H30 N6 O3
Name[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone
ChEMBL
DrugBank
ZINCZINC000208164547
PDB chain4x8c Chain A Residue 703 [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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PDB4x8c Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		V469 H471 D473 F583 P584 N585 N588 F634 V643
Binding residue
(residue number reindexed from 1)		V374 H376 D378 F483 P484 N485 N488 F527 V534
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D350 H471 D473 A645
Catalytic site (residue number reindexed from 1) D283 H376 D378 A536
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
GO:0046872 metal ion binding
GO:0140794 histone arginine deiminase activity
GO:0140795 histone H3R2 arginine deiminase activity
GO:0140796 histone H3R8 arginine deiminase activity
GO:0140797 histone H3R17 arginine deiminase activity
GO:0140798 histone H3R26 arginine deiminase activity
Biological Process
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006338 chromatin remodeling
GO:0019827 stem cell population maintenance
GO:0036211 protein modification process
GO:0043687 post-translational protein modification
GO:0045087 innate immune response
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4x8c, PDBe:4x8c, PDBj:4x8c
PDBsum4x8c
PubMed25622091
UniProtQ9UM07|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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