4UIA | pdb_00004uia

Crystal structure of 3a in complex with tafCPB

• PDB DOI: https://doi.org/10.2210/pdb4UIA/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2015-03-27 Released: 2015-06-03 
• Deposition Author(s): Halland, N., Broenstrup, M., Czech, J., Czechtizky, W., Evers, A., Follmann, M., Kohlmann, M., Schiell, M., Kurz, M., Schreuder, H.A., Kallus, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.251 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Novel Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (Tafia) from Natural Product Anabaenopeptin.

Halland, N., Bronstrup, M., Czech, J., Czechtizky, W., Evers, A., Follmann, M., Kohlmann, M., Schiell, M., Kurz, M., Schreuder, H.A., Kallus, C.

(2015) J Med Chem 58: 4839

• PubMed: 25990761 
• DOI: https://doi.org/10.1021/jm501840b
• Primary Citation Related Structures: 
  4UIA, 4UIB


• PubMed Abstract: 
  

  Anabaenopeptins isolated from cyanobacteria were identified as inhibitors of carboxypeptidase TAFIa. Cocrystal structures of these macrocyclic natural product inhibitors in a modified porcine carboxypeptidase B revealed their binding mode and provided the basis for the rational design of small molecule inhibitors with a previously unknown central urea motif. Optimization based on these design concepts allowed for a rapid evaluation of the SAR and delivered potent small molecule inhibitors of TAFIa with a promising overall profile.

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Organizational Affiliation: 
• ‡Helmholtz Institute for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany.
§Bayer Healthcare, Aprather Weg 18A, D-42113 Wuppertal, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.47 kDa 
• Atom Count: 2,806 
• Modeled Residue Count: 305 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBOXYPEPTIDASE B	A	307	Sus scrofa	Mutation(s): 8  EC: 3.4.17.2 (PDB Primary Data), 3.4.17.20 (PDB Primary Data)
UniProt
Find proteins for P09955 (Sus scrofa) Explore P09955  Go to UniProtKB:  P09955

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FH9	E [auth A]	(2S)-6-azanyl-2-[[(2R)-3-cyclohexyl-1-(3-methylbutylamino)-1-oxidanylidene-propan-2-yl]carbamoylamino]hexanoic acid C21 H40 N4 O4 PNONBGCPQRQQBB-ZWKOTPCHSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.251 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.673	α = 90
b = 83.673	β = 90
c = 97.035	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Halland, N., Broenstrup, M., Czech, J., Czechtizky, W., Evers, A., Follmann, M., Kohlmann, M., Schiell, M., Kurz, M., Schreuder, H.A., Kallus, C.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary