6TMP | pdb_00006tmp

Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures

PDB DOI: https://doi.org/10.2210/pdb6TMP/pdb

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

Deposited: 2019-12-05 Released: 2020-10-14
Deposition Author(s): Baker, L.M., Aimon, A., Murray, J.B., Surgenor, A.E., Matassova, N., Roughley, S.D., von Delft, F., Hubbard, R.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 6TMP

Ligand Structure Quality Assessment

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

Literature

Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures

Baker, L.M., Aimon, A., Murray, J.B., Surgenor, A.E., Matassova, N., Roughley, S.D., Collins, P.M., Krojer, T., von Delft, F., Hubbard, R.E.

(2020) Commun Chem

DOI: https://doi.org/10.1038/s42004-020-00367-0

Macromolecule Content

Total Structure Weight: 45.44 kDa
Atom Count: 2,977
Modeled Residue Count: 345
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial	A [auth AAA]	394	Homo sapiens	Mutation(s): 0 Gene Names: PDK2, PDHK2 EC: 2.7.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15119 (Homo sapiens) Explore Q15119 Go to UniProtKB: Q15119
PHAROS: Q15119 GTEx: ENSG00000005882
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15119
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NN8 (Subject of Investigation/LOI) Query on NN8 Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	[2,4-bis(oxidanyl)phenyl]-[(1~{R})-6,7-dimethoxy-1-pyridin-3-yl-3,4-dihydro-1~{H}-isoquinolin-2-yl]methanone C₂₃ H₂₂ N₂ O₅ CLPZEFHDKKRVHY-QFIPXVFZSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
TF3 Query on TF3 Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE C₂₀ H₂₅ Cl N₂ O₂ DFXJYVQAAFOZDP-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]

Binding Affinity Annotations
ID	Source	Binding Affinity
TF3	BindingDB: 6TMP	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.172 (Depositor), 0.172 (DCC)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.292	α = 90
b = 109.292	β = 90
c = 83.654	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.