7YUZ

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets.

Ohta, A.Tanada, M.Shinohara, S.Morita, Y.Nakano, K.Yamagishi, Y.Takano, R.Kariyuki, S.Iida, T.Matsuo, A.Ozeki, K.Emura, T.Sakurai, Y.Takano, K.Higashida, A.Kojima, M.Muraoka, T.Takeyama, R.Kato, T.Kimura, K.Ogawa, K.Ohara, K.Tanaka, S.Kikuchi, Y.Hisada, N.Hayashi, R.Nishimura, Y.Nomura, K.Tachibana, T.Irie, M.Kawada, H.Torizawa, T.Murao, N.Kotake, T.Tanaka, M.Ishikawa, S.Miyake, T.Tamiya, M.Arai, M.Chiyoda, A.Akai, S.Sase, H.Kuramoto, S.Ito, T.Shiraishi, T.Kojima, T.Iikura, H.

(2023) J Am Chem Soc 145: 24035-24051

  • DOI: https://doi.org/10.1021/jacs.3c07145
  • Primary Citation of Related Structures:  
    7YUZ, 7YV1

  • PubMed Abstract: 

    Establishing a technological platform for creating clinical compounds inhibiting intracellular protein-protein interactions (PPIs) can open the door to many valuable drugs. Although small molecules and antibodies are mainstream modalities, they are not suitable for a target protein that lacks a deep cavity for a small molecule to bind or a protein found in intracellular space out of an antibody's reach. One possible approach to access these targets is to utilize so-called middle-size cyclic peptides (defined here as those with a molecular weight of 1000-2000 g/mol). In this study, we validated a new methodology to create oral drugs beyond the rule of 5 for intracellular tough targets by elucidating structural features and physicochemical properties for drug-like cyclic peptides and developing library technologies to afford highly N -alkylated cyclic peptide hits. We discovered a KRAS inhibitory clinical compound (LUNA18) as the first example of our platform technology.


  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co., Ltd., 216, Totsuka-cho,Totsuka-ku, Yokohama 244-8602, Kanagawa, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas179Homo sapiensMutation(s): 1 
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP8784B [auth I]11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  7 Unique
IDChains TypeFormula2D DiagramParent
7T2
Query on 7T2
B [auth I]L-PEPTIDE LINKINGC10 H12 Cl N O2PHE
7TK
Query on 7TK
B [auth I]L-PEPTIDE LINKINGC8 H14 N2 O3ASP
FCL
Query on FCL
B [auth I]L-PEPTIDE LINKINGC9 H10 Cl N O2PHE
MAA
Query on MAA
B [auth I]L-PEPTIDE LINKINGC4 H9 N O2ALA
MEA
Query on MEA
B [auth I]L-PEPTIDE LINKINGC10 H13 N O2PHE
MVA
Query on MVA
B [auth I]L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
B [auth I]PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.012α = 90
b = 66.012β = 90
c = 86.33γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-15
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-22
    Changes: Database references