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 1.1 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Disintegrin and metalloproteinase domain-containing protein 17A, B270Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
50X (Subject of Investigation/LOI)
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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2010-01-21 
  • 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