1XL5

HIV-1 Protease in complex with amidhyroxysulfone

PDB DOI: https://doi.org/10.2210/pdb1XL5/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-09-30 Released: 2005-06-07
Deposition Author(s): Boettcher, J., Specker, E., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.247
R-Value Work: 0.201
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 15822136 Search on PubMed
DOI: https://doi.org/10.1002/anie.200462643

Organizational Affiliation

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 22.35 kDa
Atom Count: 1,766
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367 Go to UniProtKB: P03367
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
190 Query on 190 Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	N-{(1S)-1-(3-BROMOBENZYL)-4-[(4-BROMOPHENYL)SULFONYL]-6-METHYL-2-OXOHEPTYL}-2-(2,6-DIMETHYLPHENOXY)ACETAMIDE C₃₁ H₃₇ Br F N O₅ S RVHWPGAHEOLZNT-YTCPBCGMSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
190	Binding MOAD: 1XL5	Ki: 45 (nM) from 1 assay(s)
	BindingDB: 1XL5	Ki: 45 (nM) from 1 assay(s)
	BindingDB: 1XL5	IC50: 85 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.247
R-Value Work: 0.201
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.9	α = 90
b = 85.8	β = 90
c = 46.8	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-06-07

Deposition Author(s):

Revision History (Full details and data files)

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: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

1XL5

HIV-1 Protease in complex with amidhyroxysulfone

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)