Structure of PDB 5to3 Chain B Binding Site BS01

Receptor Information
>5to3 Chain B (length=367) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETKGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSAGAGCDRDGKYGFYTHVFRLKKWIQKVIDQ
FGGGSEPVDPCFRANCEYQCQPLNQTSYLCVCAEGFAPIPHEPHRCQMFC
NQTACPADCDPNTQASCECPEGYILDDGFICTDIDECENGGFCSGVCHNL
PGTFECICGARHIGTDC
Ligand information
Ligand ID0G6
InChIInChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
InChIKeyDVFLYEYCMMLBTQ-VSZNYVQBSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC(CCCNC(=[NH2+])\N)C(O)CCl)C2N(C(=O)C(N)Cc1ccccc1)CCC2
CACTVS 3.370N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)N[CH](CCCNC(N)=[NH2+])[CH](O)CCl
CACTVS 3.370N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(N)=[NH2+])[C@H](O)CCl
OpenEye OEToolkits 1.7.6c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
OpenEye OEToolkits 1.7.6c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(=[NH2+])N)[C@@H](CCl)O)N
FormulaC21 H34 Cl N6 O3
NameD-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide;
PPACK
ChEMBL
DrugBankDB06841
ZINC
PDB chain5to3 Chain B Residue 501 [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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PDB5to3 Rational Design of Protein C Activators.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		H58 Y62 W65 L111 D214 A215 S220 S241 A242 G243
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 D193 A194 S199 S220 A221 G222
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H58 D114 E217 G218 D219 S220 G221
Catalytic site (residue number reindexed from 1) H43 D99 E196 G197 D198 S199 G200
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0004888 transmembrane signaling receptor activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5to3, PDBe:5to3, PDBj:5to3
PDBsum5to3
PubMed28294177
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2);
P07204|TRBM_HUMAN Thrombomodulin (Gene Name=THBD)

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