4UIB

Crystal structure of 3p in complex with tafCPB

• PDB DOI: https://doi.org/10.2210/pdb4UIB/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: 1.94 Å
• R-Value Free: 0.192 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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 of 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.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.96 kDa 
• Atom Count: 3,007 
• Modelled 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
UniProt
Find proteins for P09955 (Sus scrofa) Explore P09955  Go to UniProtKB:  P09955

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GWX	J [auth A]	(2S)-6-AMINO-2-[[(1R)-1-(CYCLOHEXYLMETHYL)-2-OXO-2-[[(2S)-1,7,7-TRIMETHYLNORBORNAN-2-YL]AMINO]ETHYL]ARBAMOYLAMINO]HEXANOIC ACID C26 H46 N4 O4 AUFLFYNRNWZZKB-DMOSHBFOSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
GWX	Binding MOAD:  4UIB	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.192 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.53	α = 90
b = 82.53	β = 90
c = 95.397	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	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: 2017-09-27
  Changes: Data collection