PDBsum entry 3rml

Hydrolase/hydrolase inhibitor

PDB id: 3rml

Contents

Protein chains

28 a.a.

251 a.a.

11 a.a.

Ligands

NAG

M31

GOL ×2

PO4

Metals

_NA ×2

Waters ×297

PDB id:

3rml

Name:

Hydrolase/hydrolase inhibitor

Title:

Human thrombin in complex with mi331

Structure:

Thrombin light chain. Chain: l. Thrombin heavy chain. Chain: h. Hirudin variant-2. Chain: i. Fragment: residues in unp 60-72. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421. Other_details: synthetic fragment of hirudin from hirudo medicinalis

Resolution:

1.53Å R-factor: 0.160 R-free: 0.186

Authors:

A.Biela,A.Heine,G.Klebe

Key ref:

A.Biela et al. (2012). Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect. J Med Chem, 55, 6094-6110. PubMed id: 22612268

Date:

21-Apr-11 Release date: 25-Apr-12

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 251 a.a.

Protein chain

P09945  (HIRV2_HIRME) -  Hirudin variant-2 (Fragment) from Hirudo medicinalis

Seq: 72 a.a.

Struc: 11 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

J Med Chem 55:6094-6110 (2012)

PubMed id: 22612268

Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect.

A.Biela, F.Sielaff, F.Terwesten, A.Heine, T.Steinmetzer, G.Klebe.

ABSTRACT

Well-ordered water molecules are displaced from thrombin's hydrophobic S3/4-pocket by P3-varied ligands (Gly, d-Ala, d-Val, d-Leu to d-Cha with increased hydrophobicity and steric requirement). Two series with 2-(aminomethyl)-5-chlorobenzylamide and 4-amidinobenzylamide at P1 were examined by ITC and crystallography. Although experiencing different interactions in S1, they display almost equal potency. For both scaffolds the terminal benzylsulfonyl substituent differs in binding, whereas the increasingly bulky P3-groups address S3/4 pocket similarly. Small substituents leave the solvation pattern unperturbed as found in the uncomplexed enzyme while increasingly larger ones stepwise displace the waters. Medium-sized groups show patterns with partially occupied waters. The overall 40-fold affinity enhancement correlates with water displacement and growing number of van der Waals contacts and is mainly attributed to favorable entropy. Both Gly derivatives deviate from the series and adopt different binding modes. Nonetheless, their thermodynamic signatures are virtually identical with the homologous d-Ala derivatives. Accordingly, unchanged thermodynamic profiles are no reliable indicator for conserved binding modes.