5LYI | pdb_00005lyi

Crystal structure of 1 in complex with tafCPB

• PDB DOI: https://doi.org/10.2210/pdb5LYI/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Komagataella phaffii CBS 7435
• Mutation(s): No 


• Deposited: 2016-09-28 Released: 2016-10-26 
• Deposition Author(s): Schreuder, H., Liesum, A., Loenze, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.207 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Sulfamide as Zinc Binding Motif in Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).

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

(2016) J Med Chem 59: 9567-9573

• PubMed: 27749053 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b01276
• Primary Citation of Related Structures:  
  5LYD, 5LYF, 5LYI, 5LYL


• PubMed Abstract: 
  

  Previously disclosed TAFIa inhibitors having a urea zinc-binding motif were used as the starting point for the development of a novel class of highly potent inhibitors having a sulfamide zinc-binding motif. High-resolution X-ray cocrystal structures were used to optimize the structures and reveal a highly unusual sulfamide configuration. A selected sulfamide was profiled in vitro and in vivo and displayed a promising ADMET profile.

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Organizational Affiliation: 

Sanofi R&D , Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.57 kDa 
• Atom Count: 3,115 
• 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): 0  Gene Names: CPB1, CPB EC: 3.4.17.2
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
T4F	E [auth A]	(2~{S})-6-azanyl-2-[[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(1~{R},2~{S},4~{R})-1,7,7-trimethyl-2-bicyclo[2.2.1]hepta nyl]amino]propan-2-yl]sulfamoylamino]hexanoic acid C25 H46 N4 O5 S IQHARPQKKWCGEY-PHGOAHNDSA-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: 1.64 Å
• R-Value Free:  0.207 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.039	α = 90
b = 82.039	β = 90
c = 95.813	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Schreuder, H., Liesum, A., Loenze, P.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary