2FME | pdb_00002fme

Crystal structure of the mitotic kinesin eg5 (ksp) in complex with mg-adp and (r)-4-(3-hydroxyphenyl)-n,n,7,8-tetramethyl-3,4-dihydroisoquinoline-2(1h)-carboxamide

PDB DOI: https://doi.org/10.2210/pdb2FME/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-01-09 Released: 2006-04-18
Deposition Author(s): Sheriff, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.305 (Depositor), 0.278 (DCC)
R-Value Work:
0.280 (Depositor), 0.252 (DCC)

Starting Model: other
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

Inhibitors of human mitotic kinesin Eg5: Characterization of the 4-phenyl-tetrahydroisoquinoline lead series

Tarby, C.M., Kaltenbach III, R.F., Huynh, T., Pudzianowski, A., Shen, H., Ortega-Nanos, M., Sheriff, S., Newitt, J.A., McDonnell, P.A., Burford, N., Fairchild, C.R., Vaccaro, W., Chen, Z., Borzilleri, R.M., Naglich, J., Lombardo, L.J., Gottardis, M., Trainor, G.L., Roussell, D.L.

(2006) Bioorg Med Chem Lett 16: 2095-2100

PubMed: 16458511 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.01.056
Primary Citation Related Structures:
2FME

PubMed Abstract:
In a high-throughput screening effort, a series of tetrahydroisoquinolines was identified as modest inhibitors of human Eg5. A medicinal chemistry optimization effort led to the identification of R-4-(3-hydroxyphenyl)-N,N-7,8-tetramethyl-3,4-dihydroisoquinoline-2(1H)-carboxamide (32a) as a potent inhibitor of human Eg5 (ATPase IC50 104 nM) with good anti-proliferative activity in A2780 cells (IC50 234 nM).

Organizational Affiliation

Bristol-Myers Squibb Company, Route 206 and Province Line Road, Princeton, NJ 08543, USA. christine.tarby@bms.com

Macromolecule Content

Total Structure Weight: 83.66 kDa
Atom Count: 5,282
Modeled Residue Count: 650
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF11	A, B	368	Homo sapiens	Mutation(s): 0 Gene Names: KIF11, EG5, KNSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732 Go to UniProtKB: P52732
PHAROS: P52732 GTEx: ENSG00000138160
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
3QC Query on 3QC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	(4R)-4-(3-HYDROXYPHENYL)-N,N,7,8-TETRAMETHYL-3,4-DIHYDROISOQUINOLINE-2(1H)-CARBOXAMIDE C₂₀ H₂₄ N₂ O₂ HPVCRUIDFODATB-LJQANCHMSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
3QC	BindingDB: 2FME	IC50: 306 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.305 (Depositor), 0.278 (DCC)
R-Value Work: 0.280 (Depositor), 0.252 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.8	α = 90
b = 80	β = 96.5
c = 69.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CNX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-04-18

Deposition Author(s):

Sheriff, S.

Revision History (Full details and data files)

Version 1.0: 2006-04-18
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-04-03
Changes: Refinement description