2KP8 | pdb_00002kp8

Ligand bound to a model peptide that mimics the open fusogenic form

PDB DOI: https://doi.org/10.2210/pdb2KP8/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-09 Released: 2010-01-19
Deposition Author(s): Olejniczak, E.T.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 50
Conformers Submitted: 5
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

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

Literature

Non-peptide entry inhibitors of HIV-1 that target the gp41 coiled coil pocket.

Stewart, K.D., Huth, J.R., Ng, T.I., McDaniel, K., Hutchinson, R.N., Stoll, V.S., Mendoza, R.R., Matayoshi, E.D., Carrick, R., Mo, H., Severin, J., Walter, K., Richardson, P.L., Barrett, L.W., Meadows, R., Anderson, S., Kohlbrenner, W., Maring, C., Kempf, D.J., Molla, A., Olejniczak, E.T.

(2010) Bioorg Med Chem Lett 20: 612-617

PubMed: 20004576 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.11.076
Primary Citation of Related Structures:
2KP8

PubMed Abstract:
The ectodomain of HIV-1 gp41 mediates the fusion of viral and host cellular membranes. The peptide-based drug Enfuvirtide(1) is precedent that antagonists of this fusion activity may act as anti HIV-agents. Here, NMR screening was used to discover non-peptide leads against this target and resulted in the discovery of a new benzamide 1 series. This series is non-peptide, low molecular weight, and analogs have activity in a cell fusion assay with EC50 values ranging 3-41microM. Structural work on the gp41/benzamide 1 complex was determined by NMR spectroscopy using a designed model peptide system that mimics an open pocket of the fusogenic form of the protein.

Organizational Affiliation

Pharmaceutical Discovery Division, Abbott Laboratories, 100 Abbott Park Rd., R46Y, AP10, Abbott Park, IL 60064-6098, United States. kent.d.stewart@abbott.com

Macromolecule Content

Total Structure Weight: 25.06 kDa
Atom Count: 1,762
Modelled Residue Count: 216
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Model peptide	A, B, C	72	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XIG Query on XIG Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	5-{[(4'-methoxybiphenyl-4-yl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid C₃₄ H₂₉ N O₈ RDVWBTCVLAKXDT-PMERELPUSA-N		Interactions Focus chain D [auth B]