1HIV

CRYSTAL STRUCTURE OF A COMPLEX OF HIV-1 PROTEASE WITH A DIHYDROETHYLENE-CONTAINING INHIBITOR: COMPARISONS WITH MOLECULAR MODELING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling.

Thanki, N.Rao, J.K.Foundling, S.I.Howe, W.J.Moon, J.B.Hui, J.O.Tomasselli, A.G.Heinrikson, R.L.Thaisrivongs, S.Wlodawer, A.

(1992) Protein Sci. 1: 1061-1072

  • DOI: 10.1002/pro.5560010811

  • PubMed Abstract: 
  • The structure of a crystal complex of recombinant human immunodeficiency virus type 1 (HIV-1) protease with a peptide-mimetic inhibitor containing a dihydroxyethylene isostere insert replacing the scissile bond has been determined. The inhibitor is N ...

    The structure of a crystal complex of recombinant human immunodeficiency virus type 1 (HIV-1) protease with a peptide-mimetic inhibitor containing a dihydroxyethylene isostere insert replacing the scissile bond has been determined. The inhibitor is Noa-His-Hch psi [CH(OH)CH(OH)]Vam-Ile-Amp (U-75875), and its Ki for inhibition of the HIV-1 protease is < 1.0 nM (Noa = 1-naphthoxyacetyl, Hch = a hydroxy-modified form of cyclohexylalanine, Vam = a hydroxy-modified form of valine, Amp = 2-pyridylmethylamine). The structure of the complex has been refined to a crystallographic R factor of 0.169 at 2.0 A resolution by using restrained least-squares procedures. Root mean square deviations from ideality are 0.02 A and 2.4 degrees, for bond lengths and angles, respectively. The bound inhibitor diastereomer has the R configurations at both of the hydroxyl chiral carbon atoms. One of the diol hydroxyl groups is positioned such that it forms hydrogen bonds with both the active site aspartates, whereas the other interacts with only one of them. Comparison of this X-ray structure with a model-built structure of the inhibitor, published earlier, reveals similar positioning of the backbone atoms and of the side-chain atoms in the P2-P2' region, where the interaction with the protein is strongest. However, the X-ray structure and the model differ considerably in the location of the P3 and P3' end groups, and also in the positioning of the second of the two central hydroxyl groups. Reconstruction of the central portion of the model revealed the source of the hydroxyl discrepancy, which, when corrected, provided a P1-P1' geometry very close to that seen in the X-ray structure.


    Organizational Affiliation

    Macromolecular Structure Laboratory, NCI-Frederick Cancer Research and Development Center, ABL-Basic Research Program, Maryland 21702.




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
1ZK
Query on 1ZK

Download SDF File 
Download CCD File 
A
4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carbamoyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium
U75875
C45 H62 N7 O7
ZTKCGLWIXHAITR-JIFWBGJESA-O
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000403 (1ZK)
Query on PRD_000403
ANoa-His-Cha.psi.[CHOHCHOH]Val-Ile-Amp, U75875Peptide-like / Inhibitor

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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 %)
1ZKKi: <1 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.000α = 90.00
b = 58.600β = 90.00
c = 61.900γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other