5IVT | pdb_00005ivt

Crystal Structure of HIV Protease complexed with [(1S)-1-[(S)-(4-chlorophenyl)-(3,5-difluorophenyl)methyl]-2-[[5-fluoro-4-[2-[(2R,5S)-5-(2,2,2-trifluoroethylcarbamoyloxymethyl)morpholin-4-ium-2-yl]ethyl]pyridin-1-ium-3-yl]amino]-2-oxo-ethyl]ammonium

PDB DOI: https://doi.org/10.2210/pdb5IVT/pdb

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

Deposited: 2016-03-21 Released: 2016-05-18
Deposition Author(s): Su, H.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.193 (Depositor), 0.191 (DCC)
R-Value Work:
0.184 (Depositor), 0.179 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group.

Bungard, C.J., Williams, P.D., Ballard, J.E., Bennett, D.J., Beaulieu, C., Bahnck-Teets, C., Carroll, S.S., Chang, R.K., Dubost, D.C., Fay, J.F., Diamond, T.L., Greshock, T.J., Hao, L., Holloway, M.K., Felock, P.J., Gesell, J.J., Su, H.P., Manikowski, J.J., McKay, D.J., Miller, M., Min, X., Molinaro, C., Moradei, O.M., Nantermet, P.G., Nadeau, C., Sanchez, R.I., Satyanarayana, T., Shipe, W.D., Singh, S.K., Truong, V.L., Vijayasaradhi, S., Wiscount, C.M., Vacca, J.P., Crane, S.N., McCauley, J.A.

(2016) ACS Med Chem Lett 7: 702-707

PubMed: 27437081 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6b00135
Primary Citation Related Structures:
5IVQ, 5IVR, 5IVS, 5IVT

PubMed Abstract:
A novel HIV protease inhibitor was designed using a morpholine core as the aspartate binding group. Analysis of the crystal structure of the initial lead bound to HIV protease enabled optimization of enzyme potency and antiviral activity. This afforded a series of potent orally bioavailable inhibitors of which MK-8718 was identified as a compound with a favorable overall profile.

Organizational Affiliation

Merck Research Laboratories , 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States.

Macromolecule Content

Total Structure Weight: 23.15 kDa
Atom Count: 1,866
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 3 Gene Names: pol
UniProt
Find proteins for G0X8E8 (Human immunodeficiency virus type 1) Explore G0X8E8 Go to UniProtKB: G0X8E8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0X8E8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6EE Query on 6EE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	(betaS)-4-chloro-beta-(3,5-difluorophenyl)-N-(5-fluoro-4-{2-[(2R,5S)-5-({[(2,2,2-trifluoroethyl)carbamoyl]oxy}methyl)morpholin-2-yl]ethyl}pyridin-3-yl)-L-phenylalaninamide C₃₀ H₃₀ Cl F₆ N₅ O₄ OUUHZXOSBUCFJO-ZKBLBJRCSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.193 (Depositor), 0.191 (DCC)
R-Value Work: 0.184 (Depositor), 0.179 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.48	α = 90
b = 85.93	β = 90
c = 46.22	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Su, H.P.

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2016-08-10
Changes: Data collection, Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations