6CDJ

HIV-1 wild type protease with GRL-03314A, 6-5-5-ring fused umbrella-like tetrahydropyranofuran as the P2-ligand, a cyclopropylaminobenzothiazole as the P2'-ligand and 3,5-difluorophenylmethyl as the P1-ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis.

Ghosh, A.K.R Nyalapatla, P.Kovela, S.Rao, K.V.Brindisi, M.Osswald, H.L.Amano, M.Aoki, M.Agniswamy, J.Wang, Y.F.Weber, I.T.Mitsuya, H.

(2018) J. Med. Chem. 61: 4561-4577


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
Find proteins for Q5RZ08 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q5RZ08
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GR8
Query on GR8

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A
(2aS,4R,4aS,7aS,7bS)-octahydro-2H-1,7-dioxacyclopenta[cd]inden-4-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate
C34 H42 F2 N4 O7 S2
NIZKZMLJMFCQSW-FQOBIZQLSA-N
 Ligand Interaction
ACT
Query on ACT

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B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.959α = 90.00
b = 86.077β = 90.00
c = 46.157γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIHUnited StatesGM53386
NIHUnited StatesGM62920
National Cancer InstituteUnited Statesthe Intramural Research Program of the Center for Cancer Research
the Ministry of Education, Culture, Sports, Science, and Technology of Japan (Monbu Kagakusho)Japana Grant-in-Aid for Scientific Research (Priority Areas)
the Ministry of Health, Welfare, and Labor of JapanJapana Grant for Promotion of AIDS Research
the Ministry of Education, Culture, Sports, Science, and Technology of Japan (Monbu Kagakusho)Japanthe Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references