1ZPB

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with 4-Methyl-pentanoic acid {1-[4-guanidino-1-(thiazole-2-carbonyl)-butylcarbamoyl]-2-methyl-propyl}-amide

• PDB DOI: https://doi.org/10.2210/pdb1ZPB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2005-05-16 Released: 2006-04-18 
• Deposition Author(s): Deng, H., Bannister, T.D., Jin, L., Nagafuji, P., Celatka, C.A., Lin, J., Lazarova, T.I., Rynkiewicz, M.J., Quinn, J., Bibbins, F., Pandey, P., Gorga, J., Babine, R.E., Meyers, H.V., Abdel-Meguid, S.S., Strickler, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Synthesis, SAR exploration, and X-ray crystal structures of factor XIa inhibitors containing an alpha-ketothiazole arginine

Deng, H., Bannister, T.D., Jin, L., Babine, R.E., Quinn, J., Nagafuji, P., Celatka, C.A., Lin, J., Lazarova, T.I., Rynkiewicz, M.J., Bibbins, F., Pandey, P., Gorga, J., Meyers, H.V., Abdel-Meguid, S.S., Strickler, J.E.

(2006) Bioorg Med Chem Lett 16: 3049-3054

• PubMed: 16524727 
• DOI: https://doi.org/10.1016/j.bmcl.2006.02.052
• Primary Citation of Related Structures:  
  1ZPB, 1ZPC, 2FDA


• PubMed Abstract: 
  

  Using an alpha-ketothiazole arginine moiety as a key recognition element, a series of small peptidomimetic molecules was designed and synthesized, and their co-crystal structures with factor XIa were studied in an effort to develop smaller, less peptidic inhibitors as antithrombotic agents.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC (DAIAMED), One Kendall Square, Bldg 700, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.29 kDa 
• Atom Count: 2,107 
• Modelled Residue Count: 237 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	238	Homo sapiens	Mutation(s): 4  Gene Names: F11 EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens) Explore P03951  Go to UniProtKB:  P03951
PHAROS:  P03951 GTEx:  ENSG00000088926

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
995	C [auth A]	4-METHYL-PENTANOIC ACID {1-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYLCARBAMOYL]-2-METHYL-PROPYL}-AMIDE C20 H36 N6 O3 S ZXELQWLUDMEUHS-HOCLYGCPSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.173	α = 90
b = 121.173	β = 90
c = 121.173	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Deng, H., Bannister, T.D., Jin, L., Nagafuji, P., Celatka, C.A., Lin, J., Lazarova, T.I., Rynkiewicz, M.J., Quinn, J., Bibbins, F., Pandey, P., Gorga, J., Babine, R.E., Meyers, H.V., Abdel-Meguid, S.S., Strickler, J.E.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-10-20
  Changes: Atomic model, Database references, Derived calculations
• Version 2.1: 2023-08-23
  Changes: Data collection, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary