Structure of PDB 2dw5 Chain A Binding Site BS06

Receptor Information
>2dw5 Chain A (length=626) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GTLIRVTPEQPTHAVCVLGTLTQLDICSSAPETSFSINASPGVVVDITWP
LDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCA
DITRTGKQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQ
DMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATCSVVLGPKWPS
HYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVF
QDSVVFRVAPWIMTPNTQPPQEVYACSENEDFLKSVTTLAMKAKCKLTIC
PEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGP
DFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPS
NDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGF
RLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLRE
HNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMV
NMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYH
IRHGEVHCGTNVRRKPFSFKWWNMVP
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 chain2dw5 Chain A Residue 800 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2dw5 Inhibitors and Inactivators of Protein Arginine Deiminase 4: Functional and Structural Characterization
Resolution2.3 Å
Binding residue
(original residue number in PDB)		W347 D350 R374 V469 H471 R639 C645
Binding residue
(residue number reindexed from 1)		W310 D313 R337 V432 H434 R602 C608
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D350 H471 D473 C645
Catalytic site (residue number reindexed from 1) D313 H434 D436 C608
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
View graph for
Cellular Component
External links
PDB RCSB:2dw5, PDBe:2dw5, PDBj:2dw5
PDBsum2dw5
PubMed17002273
UniProtQ9UM07|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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