4B95

pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound

• PDB DOI: https://doi.org/10.2210/pdb4B95/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-31 Released: 2012-10-24 
• Deposition Author(s): Buckley, D.L., Gustafson, J.L., VanMolle, I., Roth, A.G., SeopTae, H., Gareiss, P.C., Jorgensen, W.L., Ciulli, A., Crews, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Small-Molecule Inhibitors of the Interaction between the E3 Ligase Vhl and Hif1Alpha

Buckley, D.L., Gustafson, J.L., Van Molle, I., Roth, A.G., Tae, H.S., Gareiss, P.C., Jorgensen, W.L., Ciulli, A., Crews, C.M.

(2012) Angew Chem Int Ed Engl 51: 11463

• PubMed: 23065727 
• DOI: https://doi.org/10.1002/anie.201206231
• Primary Citation of Related Structures:  
  4B95, 4B9K


• PubMed Abstract: 
  

  E3 ubiquitin ligases, such as the therapeutically relevant VHL, are challenging targets for traditional medicinal chemistry, as their modulation requires targeting protein-protein interactions. We report novel small-molecule inhibitors of the interaction between VHL and its molecular target HIF1α, a transcription factor involved in oxygen sensing.

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Organizational Affiliation: 

Department of Chemistry, Yale University, New Haven, CT 06511, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 172.93 kDa 
• Atom Count: 10,217 
• Modelled Residue Count: 1,309 
• Deposited Residue Count: 1,508 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2	A, D, G, J	118	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1	B, E, H, K	97	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR	C, F, I, L	162	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337  Go to UniProtKB:  P40337
PHAROS:  P40337 GTEx:  ENSG00000134086

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UCK	N [auth C], O [auth F], P [auth I], Q [auth L]	(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide C19 H18 Cl2 N2 O3 POSPLUDREYFAQC-PBHICJAKSA-N
ACT	M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
UCK	PDBBind:  4B95	IC50: 5.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.04	α = 90
b = 93.04	β = 90
c = 362.43	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Buckley, D.L., Gustafson, J.L., VanMolle, I., Roth, A.G., SeopTae, H., Gareiss, P.C., Jorgensen, W.L., Ciulli, A., Crews, C.M.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Data collection