3LGP

Crystal structure of catalytic domain of tace with benzimidazolyl-thienyl-tartrate based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and activity relationships of tartrate-based TACE inhibitors.

Li, D.Popovici-Muller, J.Belanger, D.B.Caldwell, J.Dai, C.David, M.Girijavallabhan, V.M.Lavey, B.J.Lee, J.F.Liu, Z.Mazzola, R.Rizvi, R.Rosner, K.E.Shankar, B.Spitler, J.Ting, P.C.Vaccaro, H.Yu, W.Zhou, G.Zhu, Z.Niu, X.Sun, J.Guo, Z.Orth, P.Chen, S.Kozlowski, J.A.Lundell, D.J.Madison, V.McKittrick, B.Piwinski, J.J.Shih, N.Y.Shipps, G.W.Siddiqui, M.A.Strickland, C.O.

(2010) Bioorg Med Chem Lett 20: 4812-4815

  • DOI: https://doi.org/10.1016/j.bmcl.2010.06.104
  • Primary Citation of Related Structures:  
    3LGP

  • PubMed Abstract: 

    The syntheses and structure-activity relationships of the tartrate-based TACE inhibitors are discussed. The optimization of both the prime and non-prime sites led to compounds with picomolar activity. Several analogs demonstrated good rat pharmacokinetics.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Cambridge, 320 Bent Street, Cambridge, MA 02141, United States. dansu.li@spcorp.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disintegrin and metalloproteinase domain-containing protein 17
A, B
270Homo sapiensMutation(s): 3 
Gene Names: ADAM17CSVPTACE
EC: 3.4.24.86
UniProt & NIH Common Fund Data Resources
Find proteins for P78536 (Homo sapiens)
Explore P78536 
Go to UniProtKB:  P78536
PHAROS:  P78536
GTEx:  ENSG00000151694 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78536
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
50X
Query on 50X

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
(2R,3R)-4-[(2R)-2-(3-chlorophenyl)pyrrolidin-1-yl]-2,3-dihydroxy-4-oxo-N-[(5-{[2-(trifluoromethyl)-1H-benzimidazol-1-yl]methyl}thiophen-2-yl)methyl]butanamide
C28 H26 Cl F3 N4 O4 S
JSNHRUZOJTYCCL-GMKZXUHWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
50X PDBBind:  3LGP Ki: 2 (nM) from 1 assay(s)
BindingDB:  3LGP Ki: 2 (nM) from 1 assay(s)
Binding MOAD:  3LGP Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.344α = 90
b = 76.618β = 90
c = 103.506γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-07-28 
  • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations