3M8P | pdb_00003m8p

HIV-1 RT with NNRTI TMC-125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.283 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 65BClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA. deniskertesz@comcast.net


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease H561HIV-1 M:B_HXB2RMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
p51 RT440HIV-1 M:B_HXB2RMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
65B
Query on 65B

Download Ideal Coordinates CCD File 
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 
IDSourceBinding Affinity
65B BindingDB:  3M8P Kd: 1460 (nM) from 1 assay(s)
IC50: min: 0.6, max: 3100 (nM) from 63 assay(s)
EC50: min: 2, max: 46 (nM) from 19 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.283 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.441α = 90
b = 153.533β = 90
c = 154.615γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 65BClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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