PDBsum entry 2cf8

Hydrolase/hydrolase inhibitor

PDB id: 2cf8

Contents

Protein chains

250 a.a. *

28 a.a. *

Ligands

SIN-PHE-GLU-GLU-ILE-PRO

ESH

Metals

_CA

_NA

Waters ×397

* Residue conservation analysis

PDB id:

2cf8

Name:

Hydrolase/hydrolase inhibitor

Title:

Complex of recombinant human thrombin with an inhibitor

Structure:

Thrombin heavy chain. Chain: h. Fragment: catalytic, residues 364-620. Engineered: yes. Hirudin iiia. Chain: i. Fragment: c-terminus, residues 55-65. Engineered: yes. Thrombin light chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: ovary. Synthetic: yes. Hirudo medicinalis. Medicinal leech.

Biol. unit:

Trimer (from PQS)

Resolution:

1.30Å R-factor: 0.181 R-free: 0.199

Authors:

E.Schweizer,A.Hoffmann-Roeder,J.A.Olsen,U.Obst-Sander,B.Wagner, M.Kansy,D.W.Banner,F.Diederich

Key ref:

E.Schweizer et al. (2006). Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors. Org Biomol Chem, 4, 2364-2375. PubMed id: 16763681

Date:

17-Feb-06 Release date: 14-Jun-06

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 250 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Enzyme reactions

• Enzyme class: Chains H, L: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

Org Biomol Chem 4:2364-2375 (2006)

PubMed id: 16763681

Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors.

E.Schweizer, A.Hoffmann-Röder, J.A.Olsen, P.Seiler, U.Obst-Sander, B.Wagner, M.Kansy, D.W.Banner, F.Diederich.

ABSTRACT

Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free enthalpy of protein-ligand complexation. The lactam derivatives are much more potent and more selective inhibitors (K(i) values between 0.065 and 0.005 microM, selectivity for thrombin over trypsin between 361- and 1609-fold) than the imide compounds (Ki values between 0.057 and 23.7 microM, selectivity for thrombin over trypsin between 3- and 67-fold). The increase in potency and selectivity is explained by the favorable occupancy of the P-pocket of thrombin by the additional isopropyl substituent in the lactam derivatives. The nature of the substituent on the benzyl ring filling the D pocket strongly influences binding potency in the imide series, with Ki values increasing in the sequence: F < OCH2O < Cl < H < OMe < OH < N(pyr)<< Br. This sequence can be explained by both steric fit and the occurrence of orthogonal multipolar interactions with the backbone C[double bond, length as m-dash]O moiety of Asn98. In contrast, the substituent on the benzyl ring hardly affects the ligand potency in the lactam series. This discrepancy was clarified by the comparison of X-ray structures solved for co-crystals of thrombin with imide and lactam ligands. Whereas the benzyl substituents in the imide inhibitors are sufficiently close (< or =3.5 Angstroms) to the C=O group of Asn98 to allow for attractive orthogonal multipolar interactions, the distances in the lactam series are too large (> or =4 Angstroms) for attractive dipolar contacts to be effective.