PDB Entry (3e6p)
PDB ID: 3e6p Resolution: 2.1 Å Exp. Method: X-RAY DIFFRACTION
PMID: 18854941 DOI: 10.1007/s00018-008-8502-7
Protein
Protein Name: Prothrombin
Uniprot ID/ACC: P00734 (THRB_HUMAN) Organism: Homo sapiens (Human)
Gene Symbol: F2 Gene ID: 2147
Protein Class: HYDROLASE
Ligand
Ligand Name:   D-PHENYLALANYL-N-[(1S)-4-{[(Z)-AMINO(IMINO)METHYL]AMINO}-1-(CHLOROACETYL)BUTYL]-L-PROLINAMIDE
Canonical SMILES:   N[C@H](Cc1ccccc1)C(=O)N([C@@H](CCCNC(N)=N)C(=O)CCl)C(=O)[C@@H]1CCCN1
Standard InChI:   InChI=1S/C21H31ClN6O3/c22-13-18(29)17(9-5-11-27-21(24)25)28(20(31)16-8-4-10-26-16)19(30)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-17,26H,4-5,8-13,23H2,(H4,24,25,27)/t15-,16+,17+/m1/s1
HET Code:   DFK PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C21H31ClN6O3 Mol. Weight:   450.21463 logP:   0.10337
HBD:   5 HBA:   6
#Rotatable Bonds:   11 TPSA:   154.4
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Composite Reaction HIS 57 H 26.61 5.82 Halomethyl Carbonyl
Composite Reaction SER 195 H 10.51 - Halomethyl Carbonyl
Binding Affinity
-