3NDU

HIV-1 Protease Saquinavir:Ritonavir 1:5 complex structure

PDB DOI: https://doi.org/10.2210/pdb3NDU/pdb

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

Deposited: 2010-06-08 Released: 2011-07-20
Deposition Author(s): Geremia, S., Olajuyigbe, F.M., Demitri, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.194
R-Value Work: 0.130
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures

Olajuyigbe, F.M., Demitri, N., Geremia, S.

(2011) Cryst Growth Des 11: 4378-4385

DOI: https://doi.org/10.1021/cg200514z

Macromolecule Content

Total Structure Weight: 45.6 kDa
Atom Count: 3,812
Modelled Residue Count: 398
Deposited Residue Count: 400
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, C, D	100	Human immunodeficiency virus 1	Mutation(s): 5 Gene Names: 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ROC Query on ROC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain Z [auth D]	E [auth A], Z [auth D]	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide C₃₈ H₅₀ N₆ O₅ QWAXKHKRTORLEM-UGJKXSETSA-N		Interactions Focus chain E [auth A] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Y [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth C]	I [auth A], N [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain Y [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain Y [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C]	AA [auth D], F [auth A], M [auth B], T [auth C], U [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain X [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C]	G [auth A], K [auth A], R [auth B], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C]	H [auth A] L [auth A] O [auth B] P [auth B] V [auth C] H [auth A], L [auth A], O [auth B], P [auth B], V [auth C], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B]	J [auth A], Q [auth B], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain S [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
ROC	BindingDB: 3NDU	Ki: min: 0.04, max: 138 (nM) from 29 assay(s)
		Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
		IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
		-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 47 assay(s)
		ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 47 assay(s)
		ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 44 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC) Query on PRD_000454	E [auth A], Z [auth D]	Saquinavir	Peptide-like / Inhibitor		Interactions Focus chain E [auth A] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.194
R-Value Work: 0.130
R-Value Observed: 0.136
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.19	α = 90
b = 62.705	β = 98.32
c = 59.296	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Geremia, S.

Olajuyigbe, F.M.

Demitri, N.

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2011-12-07
Changes: Database references
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary