1DMP

STRUCTURE OF HIV-1 PROTEASE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450.

Hodge, C.N.Aldrich, P.E.Bacheler, L.T.Chang, C.H.Eyermann, C.J.Garber, S.Grubb, M.Jackson, D.A.Jadhav, P.K.Korant, B.Lam, P.Y.Maurin, M.B.Meek, J.L.Otto, M.J.Rayner, M.M.Reid, C.Sharpe, T.R.Shum, L.Winslow, D.L.Erickson-Viitanen, S.

(1996) Chem.Biol. 3: 301-314


  • PubMed Abstract: 
  • Effective HIV protease inhibitors must combine potency towards wild-type and mutant variants of HIV with oral bioavailability such that drug levels in relevant tissues continuously exceed that required for inhibition of virus replication. Computer-ai ...

    Effective HIV protease inhibitors must combine potency towards wild-type and mutant variants of HIV with oral bioavailability such that drug levels in relevant tissues continuously exceed that required for inhibition of virus replication. Computer-aided design led to the discovery of cyclic urea inhibitors of the HIV protease. We set out to improve the physical properties and oral bioavailability of these compounds.


    Organizational Affiliation

    Department of Chemical Sciences, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880, USA. hodgecn@carbon.dmpc.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMQ
Query on DMQ

Download SDF File 
Download CCD File 
B
[4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-1,3-BIS([(3-AMINO)PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPINONE
DMP450(INHIBITOR OF DUPONT MERCK)
C33 H36 N4 O3
KYRSNWPSSXSNEP-ZRTHHSRSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DMQKi: 0.3 - .34 nM (98) BINDINGDB
DMQKi: 0.28 nM BINDINGMOAD
450Ki: 0.28 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.210 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.800α = 90.00
b = 62.800β = 90.00
c = 83.500γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-11-01 
  • Released Date: 1997-11-12 
  • Deposition Author(s): Chang, C.-H.

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other