3F5P

Complex Structure of Insulin-like Growth Factor Receptor and 3-Cyanoquinoline Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3F5P/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2008-11-04 Released: 2008-12-30
Deposition Author(s): Xu, W., Miller, L.M., Mayer, S.C., Berger, D.M., Boschelli, D.H., Boschelli, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.258
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Lead identification to generate 3-cyanoquinoline inhibitors of insulin-like growth factor receptor (IGF-1R) for potential use in cancer treatment

Miller, L.M., Mayer, S.C., Berger, D.M., Boschelli, D.H., Boschelli, F., Di, L., Du, X., Dutia, M., Floyd, M.B., Johnson, M., Kenny, C.H., Krishnamurthy, G., Moy, F., Petusky, S., Tkach, D., Torres, N., Wu, B., Xu, W.

(2009) Bioorg Med Chem Lett 19: 62-66

PubMed: 19041240 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.11.037
Primary Citation of Related Structures:
3F5P

PubMed Abstract:
Insulin-like growth factor receptor (IGF-1R) is a growth factor receptor tyrosine kinase that acts as a critical mediator of cell proliferation and survival. Inhibitors of this receptor are believed to provide a new target in cancer therapy. We previously reported an isoquinolinedione series of IGF-1R inhibitors. Now we have identified a series of 3-cyanoquinoline compounds that are low nanomolar inhibitors of IGF-1R. The strategies, synthesis, and SAR behind the cyanoquinoline scaffold will be discussed.

Organizational Affiliation

Wyeth Research, Chemical & Screening Sciences, Princeton, NJ, USA. millerl9@wyeth.com

Macromolecule Content

Total Structure Weight: 574.32 kDa
Atom Count: 39,086
Modelled Residue Count: 4,791
Deposited Residue Count: 4,928
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, I, J, K, L [auth M], M [auth L], N [auth R], O [auth S], P [auth T]	308	Homo sapiens	Mutation(s): 0 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
741 Query on 741 Download Ideal Coordinates CCD File SDF format, chain BA [auth M] SDF format, chain CA [auth L] SDF format, chain DA [auth R] SDF format, chain EA [auth S] SDF format, chain FA [auth T] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] SDF format, chain AA [auth K] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth R] MOL2 format, chain EA [auth S] MOL2 format, chain FA [auth T] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] MOL2 format, chain AA [auth K] mmCIF format, chain BA [auth M] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth R] mmCIF format, chain EA [auth S] mmCIF format, chain FA [auth T] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth M] CA [auth L] DA [auth R] EA [auth S] AA [auth K], BA [auth M], CA [auth L], DA [auth R], EA [auth S], FA [auth T], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	4-[[3-chloro-4-(1-methylimidazol-2-yl)sulfanyl-phenyl]amino]-7-[3-(2-hydroxyethyl-methyl-amino)propoxy]-6-methoxy-quinoline-3-carbonitrile C₂₇ H₂₉ Cl N₆ O₃ S QEMHSTOIAUCOQF-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth M] Focus chain CA [auth L] Focus chain DA [auth R] Focus chain EA [auth S] Focus chain FA [auth T] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth M] Focus chain CA [auth L] Focus chain DA [auth R] Focus chain EA [auth S] Focus chain FA [auth T] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A B C D E A, B, C, D, E, F, G, H, I, J, K, L [auth M], M [auth L], N [auth R], O [auth S], P [auth T]	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
741	BindingDB: 3F5P	IC50: 140 (nM) from 1 assay(s)
741	PDBBind: 3F5P	IC50: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.258
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.34	α = 90
b = 137.02	β = 110.36
c = 178.99	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2018-10-17
Changes: Data collection, Source and taxonomy
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Structure summary