5HZN

Structure of NVP-AEW541 in complex with IGF-1R kinase

PDB DOI: https://doi.org/10.2210/pdb5HZN/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): Yes

Deposited: 2016-02-02 Released: 2016-04-06
Deposition Author(s): Cowan-Jacob, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.218 (Depositor), 0.240 (DCC)
R-Value Work:
0.194 (Depositor), 0.220 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Identification of a 5-[3-phenyl-(2-cyclic-ether)-methylether]-4-aminopyrrolo[2,3-d]pyrimidine series of IGF-1R inhibitors.

Stauffer, F., Cowan-Jacob, S.W., Scheufler, C., Furet, P.

(2016) Bioorg Med Chem Lett 26: 2065-2067

PubMed: 26951750 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2016.02.074
Primary Citation of Related Structures:
5HHW, 5HZN

PubMed Abstract:
We report structure-guided modifications of the benzyloxy substituent of the Insulin-like Growth Factor-1 Receptor (IGF-1R) inhibitor NVP-AEW541. This chemical group has been shown to confer selectivity against other protein kinases but at the expense of a metabolism liability. X-ray crystallography has revealed that the benzyloxy moiety interacts with a lysine cation of the IGF-1R kinase domain via its ether function and its aromatic π-system and is nicely embedded in an induced hydrophobic pocket. We show that 1,4-diethers displaying an adequate hydrophobic and constrained shape are advantageous benzyloxy replacements. A single digit nanomolar inhibitor (compound 20, IC50=8.9 nM) was identified following this approach.

Organizational Affiliation

Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland. Electronic address: frederic.stauffer@novartis.com.

Macromolecule Content

Total Structure Weight: 282.32 kDa
Atom Count: 19,906
Modelled Residue Count: 2,383
Deposited Residue Count: 2,432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor	A, B, C, D, E A, B, C, D, E, F, G, H	304	Homo sapiens	Mutation(s): 2 Gene Names: IGF1R EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens) Explore P08069 Go to UniProtKB: P08069
PHAROS: P08069 GTEx: ENSG00000140443
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08069
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
66A Query on 66A Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G]	AA [auth H] I [auth A] L [auth B] N [auth C] Q [auth D] AA [auth H], I [auth A], L [auth B], N [auth C], Q [auth D], S [auth E], V [auth F], X [auth G]	7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine C₂₇ H₂₉ N₅ O AECDBHGVIIRMOI-GRGXKFILSA-N		Interactions Focus chain AA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain X [auth G]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	BA [auth H] J [auth A] M [auth B] O [auth C] R [auth D] BA [auth H], J [auth A], M [auth B], O [auth C], R [auth D], T [auth E], W [auth F], Y [auth G]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Y [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain U [auth E] SDF format, chain Z [auth G] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Z [auth G] mmCIF format, chain K [auth A] mmCIF format, chain P [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Z [auth G]	K [auth A], P [auth C], U [auth E], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain P [auth C] Focus chain U [auth E] Focus chain Z [auth G] Interactions & Density Focus chain K [auth A] Focus chain P [auth C] Focus chain U [auth E] Focus chain Z [auth G]

Binding Affinity Annotations
ID	Source	Binding Affinity
66A	BindingDB: 5HZN	IC50: min: 20, max: 86 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.218 (Depositor), 0.240 (DCC)
R-Value Work: 0.194 (Depositor), 0.220 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.435	α = 90
b = 190.045	β = 90.22
c = 155.488	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Cowan-Jacob, S.W.

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2016-12-21
Changes: Refinement description
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Refinement description