Structure of PDB 3pmh Chain B Binding Site BS01

Receptor Information

>3pmh Chain B (length=259) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQFGE

Ligand information

• Ligand ID: 0G7
• InChI: InChI=1S/C21H31ClN6O3/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/h1-3,6-7,15-17H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/t15-,16+,17+/m1/s1
• InChIKey: KWPACVJPAFGBEQ-IKGGRYGDSA-N
• SMILES:
  OpenEye OEToolkits 1.7.5: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=N)N)C(=O)CCl)N
  CACTVS 3.385: N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)N[CH](CCCNC(N)=N)C(=O)CCl
  OpenEye OEToolkits 1.7.5: [H]/N=C(\N)/NCCC[C@@H](C(=O)CCl)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](Cc2ccccc2)N
  CACTVS 3.385: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(N)=N)C(=O)CCl
  ACDLabs 12.01: O=C(NC(C(=O)CCl)CCCNC(=[N@H])N)C2N(C(=O)C(N)Cc1ccccc1)CCC2
• Formula: C21 H31 Cl N6 O3
• Name: D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide;
  d-Phe-Pro-Arg chloromethylketone (PPACK)
• ChEMBL: CHEMBL307440
• ZINC: ZINC000026376363
• PDB chain: 3pmh Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pmh Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): H57 Y60A I174 D189 A190 E192 G193 S195 W215 G216 G219
• Binding residue (residue number reindexed from 1): H43 Y47 I179 D199 A200 E202 G203 S205 W227 G228 G230
• Annotation score: 1
• Binding affinity: BindingDB: IC50=1.5nM

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D102 E192 G193 D194 S195 G196
• Catalytic site (residue number reindexed from 1): H43 D99 E202 G203 D204 S205 G206
• Enzyme Commision number: 3.4.21.5: thrombin.

Gene Ontology

Molecular Function

• GO:0004252 serine-type endopeptidase activity
• GO:0005509 calcium ion binding

Biological Process

• GO:0006508 proteolysis
• GO:0007596 blood coagulation

External links

• PDB: RCSB:3pmh, PDBe:3pmh, PDBj:3pmh
• PDBsum: 3pmh
• PubMed: 21555542
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)