2GM1

Crystal structure of the mitotic kinesin eg5 in complex with mg-adp and n-(3-aminopropyl)-n-((3-benzyl-5-chloro-4-oxo-3,4-dihydropyrrolo[2,1-f][1,2,4]triazin-2-yl)(cyclopropyl)methyl)-4-methylbenzamide

PDB DOI: https://doi.org/10.2210/pdb2GM1/pdb

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

Deposited: 2006-04-05 Released: 2006-06-27
Deposition Author(s): Sheriff, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.269 (Depositor)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Synthesis and SAR of pyrrolotriazine-4-one based Eg5 inhibitors.

Kim, K.S., Lu, S., Cornelius, L.A., Lombardo, L.J., Borzilleri, R.M., Schroeder, G.M., Sheng, C., Rovnyak, G., Crews, D., Schmidt, R.J., Williams, D.K., Bhide, R.S., Traeger, S.C., McDonnell, P.A., Mueller, L., Sheriff, S., Newitt, J.A., Pudzianowski, A.T., Yang, Z., Wild, R., Lee, F.Y., Batorsky, R., Ryder, J.S., Ortega-Nanos, M., Shen, H., Gottardis, M., Roussell, D.L.

(2006) Bioorg Med Chem Lett 16: 3937-3942

PubMed: 16730979 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.05.037
Primary Citation of Related Structures:
2GM1

PubMed Abstract:
Synthesis and SAR of substituted pyrrolotriazine-4-one analogues as Eg5 inhibitors are described. Many of these analogues displayed potent inhibitory activities in the Eg5 ATPase and A2780 cell proliferation assays. In addition, pyrrolotriazine-4-one analogue 26 demonstrated in vivo efficacy in an iv P388 murine leukemia model. Both NMR and X-ray crystallographic studies revealed that these analogues bind to an allosteric site on the Eg5 protein.

Organizational Affiliation

Department of Drug Discovery, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. kyoung.kim@bms.com

Macromolecule Content

Total Structure Weight: 168.14 kDa
Atom Count: 10,443
Modelled Residue Count: 1,297
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN-RELATED MOTOR PROTEIN EG5	A, B, C [auth D], D [auth E]	368	Homo sapiens	Mutation(s): 0 Gene Names: EG5
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52732
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2AZ Query on 2AZ Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth D] SDF format, chain S [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain S [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D] mmCIF format, chain S [auth E]	G [auth A], K [auth B], O [auth D], S [auth E]	N-(3-AMINOPROPYL)-N-[(R)-(3-BENZYL-5-CHLORO-4-OXO-3,4-DIHYDROPYRROLO[2,1-F][1,2,4]TRIAZIN-2-YL)(CYCLOPROPYL)METHYL]-4-METHYLBENZAMIDE C₂₈ H₃₀ Cl N₅ O₂ IKORZPHBTIOSSU-XMMPIXPASA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth D] Focus chain S [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth D] Focus chain S [auth E]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth D] SDF format, chain T [auth E] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] MOL2 format, chain T [auth E] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D] mmCIF format, chain T [auth E]	H [auth A], L [auth B], P [auth D], T [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth D] Focus chain T [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth D] Focus chain T [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E]	E [auth A] F [auth A] I [auth B] J [auth B] M [auth D] E [auth A], F [auth A], I [auth B], J [auth B], M [auth D], N [auth D], Q [auth E], R [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain Q [auth E] Focus chain R [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
2AZ	BindingDB: 2GM1	IC50: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.269 (Depositor)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.7	α = 90
b = 112.6	β = 90.2
c = 108.1	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-27

Deposition Author(s):

Sheriff, S.

Revision History (Full details and data files)

Version 1.0: 2006-06-27
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