2PYM

HIV-1 PR mutant in complex with nelfinavir

Structural Biology Knowledgebase: 2PYM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2PYM

Classification: HYDROLASE

Total Structure Weight: 22003.19

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASE RETROPEPSIN A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: D30N, R41A, N88D
Gene Name(s): gag-pol

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1UN
Query on 1UN

A 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)- 4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE- 3-CARBOXYLIC ACID TERT-BUTYLAMIDE
NELFINAVIR MESYLATE AG1343 (Synonym)
C32 H45 N3 O4 S
QAGYKUNXZHXKMR-HKWSIXNMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1UN Ki: 0.53 - 2 nM (86 - 95) BindingDB

Ki: 18 nM  BindingMOAD
Kd: 150 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.193
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.22 α = 90.00
b = 62.22 β = 90.00
c = 81.42 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-05-16
  • Released Date: 2008-02-26
  • Deposition author(s): Rezacova, P., Kozisek, M., Saskova, K., Brynda, J., Konvalinka, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor