Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.78 kDa 
• Atom Count: 2569 
• Modelled Residue Count: 287 
• Deposited Residue Count: 306 
• Unique protein chains: 3

2ZI2

Thrombin Inhibition

• PDB DOI: 10.2210/pdb2ZI2/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2008-02-13 Released: 2009-01-13 
• Deposition Author(s): Baum, B., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.225 
• R-Value Work: 0.181 
• R-Value Observed: 0.188 

Literature

Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry.

Baum, B., Muley, L., Smolinski, M., Heine, A., Hangauer, D., Klebe, G.

(2010) J Mol Biol 397: 1042-1054

• PubMed: 20156458 
• DOI: 10.1016/j.jmb.2010.02.007
• Primary Citation of Related Structures:  
  2ZGB, 2ZHQ, 2ZI2, 2ZNK


• PubMed Abstract: 
  

Additivity of functional group contributions to protein-ligand binding is a very popular concept in medicinal chemistry as the basis of rational design and optimized lead structures. Most of the currently applied scoring functions for docking build on such additivity models. Even though the limitation of this concept is well known, case studies examining in detail why additivity fails at the molecular level are still very scarce. The present study shows, by use of crystal structure analysis and isothermal titration calorimetry for a congeneric series of thrombin inhibitors, that extensive cooperative effects between hydrophobic contacts and hydrogen bond formation are intimately coupled via dynamic properties of the formed complexes. The formation of optimal lipophilic contacts with the surface of the thrombin S3 pocket and the full desolvation of this pocket can conflict with the formation of an optimal hydrogen bond between ligand and protein. The mutual contributions of the competing interactions depend on the size of the ligand hydrophobic substituent and influence the residual mobility of ligand portions at the binding site. Analysis of the individual crystal structures and factorizing the free energy into enthalpy and entropy demonstrates that binding affinity of the ligands results from a mixture of enthalpic contributions from hydrogen bonding and hydrophobic contacts, and entropic considerations involving an increasing loss of residual mobility of the bound ligands. This complex picture of mutually competing and partially compensating enthalpic and entropic effects determines the non-additivity of free energy contributions to ligand binding at the molecular level.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B [auth H]	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-1	C [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
24U	F [auth H]	1-butanoyl-N-(4-carbamimidoylbenzyl)-L-prolinamide C17 H24 N4 O2 RYAZZWWVNUWKNB-AWEZNQCLSA-N
BEN	G [auth H]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
NA	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	C [auth I]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
24U	Binding MOAD:  2ZI2	Ki: 5700 (nM) from 1 assay(s)
	BindingDB:  2ZI2	Ki: min: 5000, max: 5700 (nM) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000595 (24U)	F [auth H]	1-butanoyl-N-(4-carbamimidoylbenzyl)-L-prolinamide	Peptide-like / Thrombin inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.225 
• R-Value Work: 0.181 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.5	α = 90
b = 71.6	β = 100.6
c = 72.6	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-13 
• Released Date: 2009-01-13 
Deposition Author(s): Baum, B., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2016-05-25
  Changes: Source and taxonomy
• Version 1.4: 2017-10-11
  Changes: Refinement description