3EGK

KNOBLE Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3EGK/pdb

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


• Deposited: 2008-09-10 Released: 2008-09-30 
• Deposition Author(s): Baum, B., Heine, A., Klebe, G., Muenzel, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.312 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding

Gerlach, C., Munzel, M., Baum, B., Gerber, H.-D., Craan, T., Diederich, W.E., Klebe, G.

(2007) Angew Chem Int Ed Engl 46: 9105-9109

• PubMed: 17955562 
• DOI: https://doi.org/10.1002/anie.200703323
• Primary Citation of Related Structures:  
  3EGK

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Organizational Affiliation: 

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 35.75 kDa 
• Atom Count: 2,411 
• Modelled Residue Count: 285 
• Deposited Residue Count: 306 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	36	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B [auth H]	259	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000180210

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M18	D [auth H]	{(2S)-1-[N-(tert-butoxycarbonyl)glycyl]pyrrolidin-2-yl}methyl (3-chlorophenyl)acetate C20 H27 Cl N2 O5 ONXGIEJBNQLITK-INIZCTEOSA-N
NA	E [auth H], F [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
M18	PDBBind:  3EGK	Ki: 2.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.312 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.2	α = 90
b = 71.43	β = 100.52
c = 72.58	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Baum, B., Heine, A., Klebe, G., Muenzel, M.

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-09
  Changes: Derived calculations
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-10-30
  Changes: Structure summary