2XYF

HIV-1 Inhibitors with a Tertiary-Alcohol-containing Transition-State Mimic and various P2 and P1 prime Substituents

PDB DOI: https://doi.org/10.2210/pdb2XYF/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2010-11-17 Released: 2011-12-07
Deposition Author(s): Ohrngren, P., Wu, X., Persson, M., Ekegren, J.K., Wallberg, H., Rosenquist, A., Samuelsson, B., Unge, T., Larhed, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.250 (Depositor), 0.220 (DCC)
R-Value Work:
0.223 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

HIV-1 Protease Inhibitors with a Tertiary Alcohol Containing Transition-State Mimic and Various P2 and P1' Substituents

Ohrngren, P., Wu, X., Persson, M., Ekegren, J.K., Wallberg, H., Vrang, L., Rosenquist, A., Samuelsson, B., Unge, T., Larhed, M.

(2011) Medchemcomm 2: 701

DOI: https://doi.org/10.1039/C1MD00077B

Macromolecule Content

Total Structure Weight: 22.26 kDa
Atom Count: 1,704
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE	A, B	99	Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)	Mutation(s): 3 EC: 3.4.23.16
UniProt
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)) Explore P12499 Go to UniProtKB: P12499
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12499
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G40 Query on G40 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	METHYL N-[(2S)-1-[2-[(4R)-5-[[(2S)-3,3-DIMETHYL-1-METHYLAMINO-1-OXO-BUTAN-2-YL]AMINO]-4-HYDROXY-5-OXO-4-(PHENYLMETHYL)PENTYL]-2-[(4-THIOPHEN-3-YLPHENYL)METHYL]HYDRAZINYL]-3,3-DIMETHYL-1-OXO-BUTAN-2-YL]CARBAMATE C₃₈ H₅₃ N₅ O₆ S XNAIGGHDLWCRFU-SQQFMCCZSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.250 (Depositor), 0.220 (DCC)
R-Value Work: 0.223 (Depositor), 0.220 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.12	α = 90
b = 85.88	β = 90
c = 46.17	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-07
Type: Initial release
Version 1.1: 2012-04-04
Changes: Other
Version 1.2: 2018-01-17
Changes: Data collection
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description