1XL2

HIV-1 Protease in complex with pyrrolidinmethanamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An Old Target Revisited: Two New Privileged Skeletons and an Unexpected Binding Mode For HIV-Protease Inhibitors

Specker, E.Boettcher, J.Lilie, H.Heine, A.Schoop, A.Muller, G.Griebenow, N.Klebe, G.

(2005) Angew Chem Int Ed Engl 44: 3140-3144


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASE RETROPEPSINAB99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
189
Query on 189

Download CCD File 
A
N-BENZYL-2-(2,6-DIMETHYLPHENOXY)-N-[((3R,4S)-4-{[ISOBUTYL(PHENYLSULFONYL)AMINO]METHYL}PYRROLIDIN-3-YL)METHYL]ACETAMIDE
C33 H43 N3 O4 S
MQRMHPRUUKDEKO-LOYHVIPDSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
189Ki:  1500   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 57.7β = 90
c = 62.2γ = 90
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description