3E8R

Crystal structure of catalytic domain of TACE with hydroxamate inhibitor

PDB DOI: https://doi.org/10.2210/pdb3E8R/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2008-08-20 Released: 2008-10-21
Deposition Author(s): Orth, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226
R-Value Work: 0.189
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of novel hydroxamates as highly potent tumor necrosis factor-alpha converting enzyme inhibitors. Part II: optimization of the S3' pocket.

Mazzola, R.D., Zhu, Z., Sinning, L., McKittrick, B., Lavey, B., Spitler, J., Kozlowski, J., Neng-Yang, S., Zhou, G., Guo, Z., Orth, P., Madison, V., Sun, J., Lundell, D., Niu, X.

(2008) Bioorg Med Chem Lett 18: 5809-5814

PubMed: 18835710 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.09.045
Primary Citation of Related Structures:
3E8R, 3EDZ

PubMed Abstract:
A series of cyclopropyl hydroxamic acids were prepared. Many of the compounds displayed picomolar affinity for the TACE enzyme while maintaining good to excellent selectivity profiles versus MMP-1, -2, -3, -7, -14, and ADAM-10. X-ray analysis of an inhibitor in the TACE active site indicated that the molecules bound to the enzyme in the S1'-S3' pocket.

Organizational Affiliation

Department of Medicinal Chemistry, Schering Plough Research Institute, Kenilworth, NJ 07033, USA. robert.mazzola@spcorp.com

Macromolecule Content

Total Structure Weight: 63.01 kDa
Atom Count: 4,541
Modelled Residue Count: 505
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAM 17	A, B	271	Homo sapiens	Mutation(s): 3 Gene Names: ADAM17, CSVP, TACE 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78536
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
615 Query on 615 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	(1R,2S)-N~2~-hydroxy-1-{4-[(2-phenylquinolin-4-yl)methoxy]benzyl}cyclopropane-1,2-dicarboxamide C₂₈ H₂₅ N₃ O₄ BKHGWMSYWJIRLD-LXFBAYGMSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
INN Query on INN Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide C₁₉ H₃₇ N₅ O₅ LMIQCBIEAHJAMZ-GZBFAFLISA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
615	PDBBind: 3E8R	Ki: 0.18 (nM) from 1 assay(s)
615	BindingDB: 3E8R	Ki: min: 0.18, max: 0.18 (nM) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000919 (INN) Query on PRD_000919	E [auth A]	3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE	Peptide-like / Enzyme inhibitor		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226
R-Value Work: 0.189
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.722	α = 90
b = 75.761	β = 90
c = 102.985	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Orth, P.

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2013-02-27
Changes: Other
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations