3O64 | pdb_00003o64

Crystal structure of catalytic domain of TACE with 2-(2-Aminothiazol-4-yl)pyrrolidine-Based Tartrate Diamides

PDB DOI: https://doi.org/10.2210/pdb3O64/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2010-07-28 Released: 2011-04-20
Deposition Author(s): Orth, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.218 (Depositor), 0.210 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

2-(2-Aminothiazol-4-yl)pyrrolidine-based tartrate diamides as potent, selective and orally bioavailable TACE inhibitors.

Dai, C., Li, D., Popovici-Muller, J., Zhao, L., Girijavallabhan, V.M., Rosner, K.E., Lavey, B.J., Rizvi, R., Shankar, B.B., Wong, M.K., Guo, Z., Orth, P., Strickland, C.O., Sun, J., Niu, X., Chen, S., Kozlowski, J.A., Lundell, D.J., Piwinski, J.J., Shih, N.Y., Siddiqui, M.A.

(2011) Bioorg Med Chem Lett 21: 3172-3176

PubMed: 21458257 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.01.002
Primary Citation of Related Structures:
3O64

PubMed Abstract:
TNF-α converting enzyme (TACE) inhibitors are promising agents to treat inflammatory disorders and cancer. We have investigated novel tartrate diamide TACE inhibitors where the tartrate core binds to zinc in a unique tridentate fashion. Incorporating (R)-2-(2-N-alkylaminothiazol-4-yl)pyrrolidines into the left hand side amide of the tartrate scaffold led to the discovery of potent and selective TACE inhibitors, some of which exhibited good rat oral bioavailability.

Organizational Affiliation

Department of Chemistry, Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA. chaoyang.dai@merck.com

Macromolecule Content

Total Structure Weight: 62.59 kDa
Atom Count: 4,250
Modeled Residue Count: 505
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TACE	A, B	270	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
786 Query on 786 Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(2R,3R)-2,3-dihydroxy-4-{(2R)-2-[2-(methylamino)-5-(methylsulfonyl)-1,3-thiazol-4-yl]pyrrolidin-1-yl}-4-oxo-N-{(1R)-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}butanamide C₂₄ H₃₀ N₆ O₆ S₂ QFHBCQAIZQPRLF-SJFSSXKUSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
INN Query on INN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [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 D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
786	BindingDB: 3O64	Ki: 0.4 (nM) from 1 assay(s)
786	BindingDB: 3O64	IC50: 720 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000919 (INN) Query on PRD_000919	D [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 D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.218 (Depositor), 0.210 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.446	α = 90
b = 76.508	β = 90
c = 103.866	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-04-20

Deposition Author(s):

Orth, P.

Revision History (Full details and data files)

Version 1.0: 2011-04-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary