5MB0

Cocktail experiment A: fragments 63, 267, and 291 in complex with Endothiapepsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Comparison of cocktail versus single soaking experimets

Radeva, N.Heine, A.Klebe, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endothiapepsin330Cryphonectria parasiticaMutation(s): 0 
EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica)
Explore P11838 
Go to UniProtKB:  P11838
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11838
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F91
Query on F91

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
N-(pyridin-4-ylmethyl)-2,3-dihydro-1,4-benzodioxin-6-amine
C14 H14 N2 O2
ZEHRBOVXNPCYAK-UHFFFAOYSA-N
47V
Query on 47V

Download Ideal Coordinates CCD File 
I [auth A]2,5-dimethyl-N-(pyridin-4-yl)furan-3-carboxamide
C12 H12 N2 O2
LSWLYNGTJMNMRF-UHFFFAOYSA-N
F63
Query on F63

Download Ideal Coordinates CCD File 
L [auth A]N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine
C11 H12 N2 O2
MUKCVLFJCGZPKF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
F63 Binding MOAD:  5MB0 Kd: 5.00e+5 (nM) from 1 assay(s)
F91 Binding MOAD:  5MB0 Kd: 1.40e+6 (nM) from 1 assay(s)
47V Binding MOAD:  5MB0 Kd: 7.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.377α = 90
b = 73.079β = 109.59
c = 52.529γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BMBFGermany05K13RM1

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description