4MC9 | pdb_00004mc9

HIV protease in complex with AA74

PDB DOI: https://doi.org/10.2210/pdb4MC9/pdb

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

Deposited: 2013-08-21 Released: 2014-04-02
Deposition Author(s): Ganguly, A.K., Alluri, S.S., Wang, C., Antropow, A., White, A., Caroccia, D., Biswas, D., Kang, E., Zhang, L., Carroll, S.S., Burlein, C., Munshi, V., Orth, P., Strickland, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.195 (Depositor), 0.202 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural Optimization of Cyclic Sulfonamide based Novel HIV-1 Protease Inhibitors to Pico Molar Affinities guided by X-ray Crystallographic Analysis

Ganguly, A.K., Alluri, S.S., Wang, C.H., Antropow, A., White, A., Caroccia, D., Biswas, D., Kang, E., Zhang, L.K., Carroll, S.S., Burlein, C., Fay, J., Orth, P., Strickland, C.

(2014) Tetrahedron

DOI: https://doi.org/10.1016/j.tet.2014.03.038

Macromolecule Content

Total Structure Weight: 22.91 kDa
Atom Count: 1,861
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 3 Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P0C6F2 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123)) Explore P0C6F2 Go to UniProtKB: P0C6F2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6F2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
23L Query on 23L Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	(3S)-tetrahydrofuran-3-yl {(2S,3R)-4-[(4R)-7-fluoro-1,1-dioxido-4-(propan-2-yl)-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate C₂₇ H₃₅ F N₂ O₆ S NTBLOIDJWKXDON-BELIEFIBSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.195 (Depositor), 0.202 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.71	α = 90
b = 85.82	β = 90
c = 46.21	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.