3M8P

HIV-1 RT with NNRTI TMC-125

• PDB DOI: https://doi.org/10.2210/pdb3M8P/pdb

• Classification: TRANSFERASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-18 Released: 2010-05-19 
• Deposition Author(s): Harris, S.F., Villasenor, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.283 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-benzyl derivatives with broad potency against resistant mutant viruses.

Kertesz, D.J., Brotherton-Pleiss, C., Yang, M., Wang, Z., Lin, X., Qiu, Z., Hirschfeld, D.R., Gleason, S., Mirzadegan, T., Dunten, P.W., Harris, S.F., Villasenor, A.G., Hang, J.Q., Heilek, G.M., Klumpp, K.

(2010) Bioorg Med Chem Lett 20: 4215-4218

• PubMed: 20538456 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.040
• Primary Citation of Related Structures:  
  3M8P, 3M8Q, 3NBP


• PubMed Abstract: 
  

  An analysis of the binding motifs of known HIV-1 non-nucleoside reverse transcriptase inhibitors has led to discovery of novel piperidine-linked aminopyrimidine derivatives with broad activity against wild-type as well as drug-resistant mutant viruses. Notably, the series retains potency against the K103N/Y181C and Y188L mutants, among others. Thus, the N-benzyl compound 5k has a particularly attractive profile. Synthesis and SAR are presented and discussed, as well as crystal structures relating to the binding motifs.

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Organizational Affiliation: 

Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 116.54 kDa 
• Atom Count: 8,138 
• Modelled Residue Count: 952 
• Deposited Residue Count: 1,001 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	561	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B	440	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
65B	C [auth A]	4-({6-AMINO-5-BROMO-2-[(4-CYANOPHENYL)AMINO]PYRIMIDIN-4-YL}OXY)-3,5-DIMETHYLBENZONITRILE C20 H15 Br N6 O PYGWGZALEOIKDF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
65B	BindingDB:  3M8P	Kd: 1460 (nM) from 1 assay(s)
		IC50: min: 0.6, max: 3100 (nM) from 61 assay(s)
		EC50: min: 2, max: 46 (nM) from 19 assay(s)
	PDBBind:  3M8P	IC50: 2.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.283 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.441	α = 90
b = 153.533	β = 90
c = 154.615	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Harris, S.F., Villasenor, A.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-18
  Changes: Non-polymer description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations