4MC6 | pdb_00004mc6

HIV protease in complex with SA499

• PDB DOI: https://doi.org/10.2210/pdb4MC6/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.3 kDa 
• Atom Count: 1,885 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
23K	C [auth A]	1-tert-butyl-3-{(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}urea C27 H38 F N3 O4 S VQJKWPDMRXMXDB-OEMFJLHTSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.98	α = 90
b = 85.86	β = 90
c = 46.28	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

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