Structure of PDB 4x8g Chain A Binding Site BS05

Receptor Information
>4x8g Chain A (length=606) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDI
ASTWPLDPGVEVTLTMKVASGSTGDQKVQISYYPVKALLYLTGVEISLCA
DITRTGKVKPTAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDE
VLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATKCS
VVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSN
LELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACFENEDFLKSVTTLAM
KAKCKLTIQDEMEIGYIQAPHKTLPVVFDSPRKRVMGPDFGYVTRISGLD
SFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQ
VQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQ
NEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKR
ELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPV
INGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIGEVHAGTNVRRKPFSFK
WWNMVP
Ligand information
Ligand ID3Z0
InChIInChI=1S/C24H28N6O2/c1-4-30-19(12-15-7-5-9-26-22(15)30)23-27-18-11-16(13-20(32-3)21(18)28(23)2)24(31)29-10-6-8-17(25)14-29/h5,7,9,11-13,17H,4,6,8,10,14,25H2,1-3H3/t17-/m1/s1
InChIKeyJCCVZBCVMBEDEN-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCn1c(cc2cccnc12)c3nc4cc(cc(OC)c4n3C)C(=O)N5CCC[C@@H](N)C5
CACTVS 3.385CCn1c(cc2cccnc12)c3nc4cc(cc(OC)c4n3C)C(=O)N5CCC[CH](N)C5
OpenEye OEToolkits 1.9.2CCn1c(cc2c1nccc2)c3nc4cc(cc(c4n3C)OC)C(=O)N5CCC[C@H](C5)N
ACDLabs 12.01O=C(c4cc3nc(c2cc1cccnc1n2CC)n(c3c(OC)c4)C)N5CCCC(N)C5
OpenEye OEToolkits 1.9.2CCn1c(cc2c1nccc2)c3nc4cc(cc(c4n3C)OC)C(=O)N5CCCC(C5)N
FormulaC24 H28 N6 O2
Name[(3R)-3-aminopiperidin-1-yl][2-(1-ethyl-1H-pyrrolo[2,3-b]pyridin-2-yl)-7-methoxy-1-methyl-1H-benzimidazol-5-yl]methanone
ChEMBL
DrugBank
ZINCZINC000208156660
PDB chain4x8g Chain A Residue 705 [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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PDB4x8g Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation.
Resolution3.29 Å
Binding residue
(original residue number in PDB)		H471 D473 E474 A581 F582 F583 P584 N585 N588 F634 V643
Binding residue
(residue number reindexed from 1)		H416 D418 E419 A526 F527 F528 P529 N530 N533 F579 V586
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.00,IC50=1uM
Enzymatic activity
Catalytic site (original residue number in PDB) D350 H471 D473 A645
Catalytic site (residue number reindexed from 1) D310 H416 D418 A588
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4x8g, PDBe:4x8g, PDBj:4x8g
PDBsum4x8g
PubMed25622091
UniProtQ9UM07|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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