4B6L | pdb_00004b6l

Discovery of Oral Polo-Like Kinase (PLK) Inhibitors with Enhanced Selectivity Profile using Residue Targeted Drug Design

PDB DOI: https://doi.org/10.2210/pdb4B6L/pdb

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

Deposited: 2012-08-14 Released: 2013-08-21
Deposition Author(s): Brown, K., Charrier, J.D., Durrant, S., Griffiths, M., Hudson, C., Kay, D., Knegtel, R., ODonnell, M., Pierard, F., Twin, H., Weber, P., Young, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.289 (Depositor)
R-Value Work:
0.244 (Depositor), 0.245 (DCC)
R-Value Observed:
0.246 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of Oral Polo-Like Kinase (Plk) Inhibitors with Enhanced Selectivity Profile Using Residue Targeted Drug Design

Brown, K., Charrier, J.D., Durrant, S., Griffiths, M., Hudson, C., Kay, D., Knegtel, R., Odonnell, M., Pierard, F., Twin, H., Weber, P., Young, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.79 kDa
Atom Count: 2,537
Modeled Residue Count: 281
Deposited Residue Count: 281
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE PLK3	A	281	Homo sapiens	Mutation(s): 0 EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4B4 (Homo sapiens) Explore Q9H4B4 Go to UniProtKB: Q9H4B4
PHAROS: Q9H4B4 GTEx: ENSG00000173846
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H4B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9ZP Query on 9ZP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-[[(4R)-5-cyclopentyl-4-ethyl-3a,4-dihydro-3H-[1,2,4]triazolo[4,3-f]pteridin-7-yl]amino]-N-cyclopropyl-3-methoxy-benzamide C₂₅ H₃₂ N₈ O₂ BNAAGNVFCJFJIF-AUSIDOKSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.289 (Depositor)
R-Value Work: 0.244 (Depositor), 0.245 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.14	α = 90
b = 56.37	β = 96.83
c = 45.32	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other