1C1B | pdb_00001c1b

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GCA-186

PDB DOI: https://doi.org/10.2210/pdb1C1B/pdb

Classification: TRANSFERASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1999-07-21 Released: 2000-07-21
Deposition Author(s): Hopkins, A.L., Ren, J., Tanaka, H., Baba, B., Okamato, M., Stuart, D.I., Stammers, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.255 (Depositor)
R-Value Work:
0.198 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants.

Hopkins, A.L., Ren, J., Tanaka, H., Baba, M., Okamato, M., Stuart, D.I., Stammers, D.K.

(1999) J Med Chem 42: 4500-4505

PubMed: 10579814 Search on PubMed
DOI: https://doi.org/10.1021/jm990192c
Primary Citation Related Structures:
1C1B, 1C1C

PubMed Abstract:
Two analogues of the nonnucleoside inhibitor of HIV-1 RT, MKC-442 (emivirine), containing different C6 substituents have been designed to be less susceptible to the commonly found drug-resistance mutation of Tyr181Cys. Compound TNK-6123 had a C6 thiocyclohexyl group designed to have more flexibility in adapting to the mutated drug-binding site. GCA-186 had additional 3',5'-dimethyl substituents aimed at forming close contacts with the conserved residue Trp229. Both compounds showed approximately 30-fold greater inhibitory effect than MKC-442 to the Tyr181Cys mutant virus as well as to the clinically important Lys103Asn virus. X-ray crystallographic structure determination of complexes with HIV-1 RT confirmed the predicted binding modes. These strategies might be used to improve the resilience of other NNRTI series against common drug-resistance mutations.

Organizational Affiliation

Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.

Macromolecule Content

Total Structure Weight: 116.28 kDa
Atom Count: 7,888
Modeled Residue Count: 952
Deposited Residue Count: 1,000
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE (A-CHAIN)	A	560	Human immunodeficiency virus 1	Mutation(s): 1 EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE (B-CHAIN)	B	440	Human immunodeficiency virus 1	Mutation(s): 0 EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCA Query on GCA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	6-(3',5'-DIMETHYLBENZYL)-1-ETHOXYMETHYL-5-ISOPROPYLURACIL C₁₉ H₂₆ N₂ O₃ NVGVZWUORYLPAL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
GCA	BindingDB: 1C1B	EC50: 0.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.255 (Depositor)
R-Value Work: 0.198 (Depositor), 0.189 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140	α = 90
b = 111.5	β = 90
c = 73.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2000-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-07-21
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2014-11-12
Changes: Non-polymer description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary