3L0T | pdb_00003l0t

Crystal structure of catalytic domain of TACE with hydantoin inhibitor

PDB DOI: https://doi.org/10.2210/pdb3L0T/pdb

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

Deposited: 2009-12-10 Released: 2010-03-02
Deposition Author(s): Orth, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Discovery and SAR of hydantoin TACE inhibitors.

Yu, W., Guo, Z., Orth, P., Madison, V., Chen, L., Dai, C., Feltz, R.J., Girijavallabhan, V.M., Kim, S.H., Kozlowski, J.A., Lavey, B.J., Li, D., Lundell, D., Niu, X., Piwinski, J.J., Popovici-Muller, J., Rizvi, R., Rosner, K.E., Shankar, B.B., Shih, N.Y., Siddiqui, M.A., Sun, J., Tong, L., Umland, S., Wong, M.K., Yang, D.Y., Zhou, G.

(2010) Bioorg Med Chem Lett 20: 1877-1880

PubMed: 20172725 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.01.148
Primary Citation of Related Structures:
3L0T, 3L0V

PubMed Abstract:
We disclose inhibitors of TNF-alpha converting enzyme (TACE) designed around a hydantoin zinc binding moiety. Crystal structures of inhibitors bound to TACE revealed monodentate coordination of the hydantoin to the zinc. SAR, X-ray, and modeling designs are described. To our knowledge, these are the first reported X-ray structures of TACE with a hydantoin zinc ligand.

Organizational Affiliation

Department of Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA. wensheng.yu@spcorp.com

Macromolecule Content

Total Structure Weight: 62.04 kDa
Atom Count: 4,244
Modeled Residue Count: 508
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
Disintegrin and metalloproteinase domain-containing protein 17	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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]
Z94 Query on Z94 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]	N-{4-[(4S)-2,5-dioxoimidazolidin-4-yl]phenyl}acetamide C₁₁ H₁₁ N₃ O₃ GUTQNQMNYWTMBT-VIFPVBQESA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [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]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

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]