4NVN

Predicting protein conformational response in prospective ligand discovery

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.

Fischer, M., Coleman, R.G., Fraser, J.S., Shoichet, B.K.

(2014) Nat Chem 6: 575-583

  • DOI: 10.1038/nchem.1954
  • Primary Citation of Related Structures:  
    4OQ7, 4NVL, 4NVM, 4NVN, 4NVO, 4NVD, 4NVE, 4NVF, 4NVG, 4NVH

  • PubMed Abstract: 

    • Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe ...

    Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.

    Organizational Affiliation: 

    1] Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, USA [2] Faculty of Pharmacy, Donnelly Center, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1 Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c peroxidaseB289Saccharomyces cerevisiae RM11-1aMutation(s): 2 
Gene Names: CCP1 CCP CPO YKR066C, SCRG_04081
EC: 1.11.1
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LRE1 
Go to UniProtKB:  B3LRE1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download CCD File 
B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
2O1
Query on 2O1
Download CCD File 
B
2,3-dihydrobenzo[h][1,6]naphthyridin-4(1H)-one
C12 H10 N2 O
PTMYWDHBZAMKMN-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51α = 90
b = 73.44β = 90
c = 104.39γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references