3UY9

Bovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.

Tziridis, A., Rauh, D., Neumann, P., Kolenko, P., Menzel, A., Brauer, U., Ursel, C., Steinmetzer, P., Sturzebecher, J., Schweinitz, A., Steinmetzer, T., Stubbs, M.T.

(2014) Biol Chem 395: 891-903

  • DOI: https://doi.org/10.1515/hsz-2014-0158
  • Primary Citation of Related Structures:  
    3PLB, 3PLK, 3PLP, 3PM3, 3PMJ, 3PWB, 3PWC, 3PYH, 3Q00, 3UNQ, 3UNS, 3UOP, 3UPE, 3UQO, 3UQV, 3UUZ, 3UWI, 3UY9, 3V12, 3V13

  • PubMed Abstract: 

    • A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward ...

    A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cationic trypsin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
223Bos taurusMutation(s): 10 
Gene Names: PRSS1, TRP1, TRY1, TRYP1
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN
Download Ideal Coordinates CCD File 
CA [auth F],
EA [auth G],
HA [auth H],
JA [auth I],
LA [auth J],
CA [auth F],
EA [auth G],
HA [auth H],
JA [auth I],
LA [auth J],
NA [auth K],
PA [auth L],
R [auth A],
RA [auth M],
T [auth B],
TA [auth N],
V [auth C],
VA [auth O],
X [auth D],
XA [auth P],
Z [auth E]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
BA [auth F],
DA [auth G],
FA [auth H],
IA [auth I],
KA [auth J],
BA [auth F],
DA [auth G],
FA [auth H],
IA [auth I],
KA [auth J],
MA [auth K],
OA [auth L],
Q [auth A],
QA [auth M],
S [auth B],
SA [auth N],
U [auth C],
UA [auth O],
W [auth D],
WA [auth P],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
AA [auth E],
GA [auth H],
YA [auth P]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.069α = 89.62
b = 98.569β = 88.85
c = 120.781γ = 103.99
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references
  • Version 1.2: 2018-12-05
    Changes: Data collection, Source and taxonomy