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 7YV1 | pdb_00007yv1

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.277 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YV1

Ligand Structure Quality Assessment 


This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 69.43 kDa 
  • Atom Count: 5,857 
  • Modeled Residue Count: 615 
  • Deposited Residue Count: 629 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  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
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UniProt GroupP01116
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KA30L Fab H-chainB [auth H]225Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
KA30L Fab L-chainC [auth L]214Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
LUNA18D [auth I]11synthetic constructMutation(s): 0 
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Reference Sequence

Small Molecules

Modified Residues  5 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
MLE
Query on MLE
LEUMethylationC7 H15 N O2
MAA
Query on MAA
ALAMethylationC4 H9 N O2
7VU
Query on 7VU
PHEEthylationC12 H17 N O2
7VU
Query on 7VU
PHEMethylationC12 H17 N O2
SAR
Query on SAR
GLYMethylationC3 H7 N O2
Non-standard Monomers  4 Unique
IDChains TypeFormula2D Diagram
02A
Query on 02A
L-PEPTIDE LINKINGC4 H7 N O2
7VN
Query on 7VN
L-PEPTIDE LINKINGC8 H15 N O2
7W2
Query on 7W2
L-PEPTIDE LINKINGC11 H10 F5 N O2
AC5
Query on AC5
PEPTIDE LINKINGC6 H11 N O2

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.277 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.617α = 90
b = 90.373β = 90
c = 116.81γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-22
    Changes: Database references
  • Version 2.2: 2026-03-04
    Changes: Refinement description, Structure summary