Structure of PDB 3b1u Chain A Binding Site BS01

Receptor Information
>3b1u Chain A (length=628) 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
QDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLT
ICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVM
GPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCY
PSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRK
GFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTL
REHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPN
MVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFT
YHIRHGEVHCGTNVRRKPFSFKWWNMVP
Ligand information
Ligand IDYFF
InChIInChI=1S/C15H19FN4O4/c16-8-12(17)19-7-3-6-11(13(18)21)20-14(22)9-4-1-2-5-10(9)15(23)24/h1-2,4-5,11H,3,6-8H2,(H2,17,19)(H2,18,21)(H,20,22)(H,23,24)/t11-/m0/s1
InChIKeyHBEIARVCIYYMOR-NSHDSACASA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=O)[C@H](CCCNC(=N)CF)NC(=O)c1ccccc1C(O)=O
CACTVS 3.370NC(=O)[CH](CCCNC(=N)CF)NC(=O)c1ccccc1C(O)=O
OpenEye OEToolkits 1.7.2c1ccc(c(c1)C(=O)NC(CCCNC(=N)CF)C(=O)N)C(=O)O
OpenEye OEToolkits 1.7.2[H]/N=C(/CF)\NCCC[C@@H](C(=O)N)NC(=O)c1ccccc1C(=O)O
ACDLabs 12.01FCC(=[N@H])NCCCC(C(=O)N)NC(=O)c1ccccc1C(=O)O
FormulaC15 H19 F N4 O4
Name2-{[(2S)-1-amino-5-{[(1Z)-2-fluoroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid;
o-F-amidine
ChEMBLCHEMBL1962643
DrugBank
ZINCZINC000073138537
PDB chain3b1u Chain A Residue 800 [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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PDB3b1u The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors
Resolution2.1 Å
Binding residue
(original residue number in PDB)		W347 D350 R374 V469 H471 D473 R639 H640 C645
Binding residue
(residue number reindexed from 1)		W312 D315 R339 V434 H436 D438 R604 H605 C610
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.72,IC50=1.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) D350 H471 D473 C645
Catalytic site (residue number reindexed from 1) D315 H436 D438 C610
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:3b1u, PDBe:3b1u, PDBj:3b1u
PDBsum3b1u
PubMed21882827
UniProtQ9UM07|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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