7PPG | pdb_00007ppg

CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH COMPOUND 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.302 (Depositor), 0.307 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PPG

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A Novel NAMPT Inhibitor-Based Antibody-Drug Conjugate Payload Class for Cancer Therapy.

Bohnke, N.Berger, M.Griebenow, N.Rottmann, A.Erkelenz, M.Hammer, S.Berndt, S.Gunther, J.Wengner, A.M.Stelte-Ludwig, B.Mahlert, C.Greven, S.Dietz, L.Jorissen, H.Barak, N.Bomer, U.Hillig, R.C.Eberspaecher, U.Weiske, J.Giese, A.Mumberg, D.Nising, C.F.Weinmann, H.Sommer, A.

(2022) Bioconjug Chem 33: 1210-1221

  • DOI: https://doi.org/10.1021/acs.bioconjchem.2c00178
  • Primary Citation Related Structures: 
    7PPE, 7PPF, 7PPG, 7PPH, 7PPI

  • PubMed Abstract: 

    Inhibition of intracellular nicotinamide phosphoribosyltransferase (NAMPT) represents a new mode of action for cancer-targeting antibody-drug conjugates (ADCs) with activity also in slowly proliferating cells. To extend the repertoire of available effector chemistries, we have developed a novel structural class of NAMPT inhibitors as ADC payloads. A structure-activity relationship-driven approach supported by protein structural information was pursued to identify a suitable attachment point for the linker to connect the NAMPT inhibitor with the antibody. Optimization of scaffolds and linker structures led to highly potent effector chemistries which were conjugated to antibodies targeting C4.4a (LYPD3), HER2 (c-erbB2), or B7H3 (CD276) and tested on antigen-positive and -negative cancer cell lines. Pharmacokinetic studies, including metabolite profiling, were performed to optimize the stability and selectivity of the ADCs and to evaluate potential bystander effects. Optimized NAMPTi-ADCs demonstrated potent in vivo antitumor efficacy in target antigen-expressing xenograft mouse models. This led to the development of highly potent NAMPT inhibitor ADCs with a very good selectivity profile compared with the corresponding isotype control ADCs. Moreover, we demonstrate─to our knowledge for the first time─the generation of NAMPTi payload metabolites from the NAMPTi-ADCs in vitro and in vivo . In conclusion, NAMPTi-ADCs represent an attractive new payload class designed for use in ADCs for the treatment of solid and hematological cancers.


  • Organizational Affiliation
    • Bayer AG, Pharmaceuticals, Berlin 13353, Germany.

Macromolecule Content 

  • Total Structure Weight: 225.19 kDa 
  • Atom Count: 16,462 
  • Modeled Residue Count: 1,867 
  • Deposited Residue Count: 1,968 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B, C, D
492Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
GTEx:  ENSG00000105835 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7YX
(Subject of Investigation/LOI)

Query on 7YX



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
O [auth C],
S [auth D]
N-[4-[(4R)-1-cyclopentyl-4-methyl-6-oxidanylidene-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide
C24 H27 N5 O2
NMKKGESQLXZFPK-MRXNPFEDSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
K [auth B]
M [auth C]
N [auth C]
E [auth A],
F [auth A],
K [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth B],
P [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.302 (Depositor), 0.307 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.956α = 90
b = 106.18β = 96.53
c = 121.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-06-15 
  • Deposition Author(s): Hillig, R.C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-22
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description