PDBsum entry 4ufe

Hydrolase

PDB id: 4ufe

Contents

Protein chains

251 a.a.

11 a.a.

28 a.a.

Ligands

3ZD

PO4

NAG

Metals

_NA ×2

Waters ×290

PDB id:

4ufe

Name:

Hydrolase

Title:

Thrombin in complex with (2r)-2-(benzylsulfonylamino)-n-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-butyl)-3-phenyl-propanamide

Structure:

Thrombin heavy chain. Chain: h. Fragment: residues 364-621. Hirudin variant-2. Chain: i. Fragment: residues 61-72. Engineered: yes. Other_details: hirudin (54-65) (sulfated). Thrombin light chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Other_details: purified from human blood plasma. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421. Other_details: purified from human blood plasma

Resolution:

1.59Å R-factor: 0.159 R-free: 0.182

Authors:

E.Ruehmann,A.Heine,G.Klebe

Key ref:

E.H.Rühmann et al. (2016). Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures. Chemmedchem, 11, 309-319. PubMed id: 26762840 DOI: 10.1002/cmdc.201500531

Date:

16-Mar-15 Release date: 27-Jan-16

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.*

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

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

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.

DOI no: 10.1002/cmdc.201500531

Chemmedchem 11:309-319 (2016)

PubMed id: 26762840

Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.

E.H.Rühmann, M.Rupp, M.Betz, A.Heine, G.Klebe.

ABSTRACT

Structural preorganization to fix bioactive conformations at protein binding sites is a popular strategy to enhance binding affinity during late-stage optimization. The rationale for this enhancement relates to entropic advantages assigned to rigidified versus flexible ligands. We analyzed a narrow series of peptidomimetics binding to thrombin. The individual ligands exhibit at P2 a conformationally flexible glycine, more restricted alanine, N-methylglycine, N-methylhomoalanine, and largely rigidified proline moiety. Overall, affinity was found to increase by a factor of 1000, explained partly by an entropic advantage. All ligands adopt the same binding mode with small deviations. The residual mobility of the bound ligands is decreased across the series, and a protein side chain differs in its order/disorder behavior along with changes in the surface-water network pattern established across the newly generated protein-ligand surfaces. The enthalpy/entropy inventory displays a rather complex picture and emphasizes that thermodynamics can only be compared in terms of relative differences within a structurally similar ligand series.