7VBX | pdb_00007vbx

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20

PDB DOI: https://doi.org/10.2210/pdb7VBX/pdb

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

Deposited: 2021-09-01 Released: 2022-02-16
Deposition Author(s): Orita, T., Doi, S., Iwanaga, T., Fujishima, A., Adachi, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.251 (Depositor), 0.254 (DCC)
R-Value Work:
0.224 (Depositor), 0.224 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-based drug design of novel and highly potent pyruvate dehydrogenase kinase inhibitors.

Bessho, Y., Akaki, T., Hara, Y., Yamakawa, M., Obika, S., Mori, G., Ubukata, M., Yasue, K., Nakane, Y., Terasako, Y., Orita, T., Doi, S., Iwanaga, T., Fujishima, A., Adachi, T., Ueno, H., Motomura, T.

(2021) Bioorg Med Chem 52: 116514

DOI: https://doi.org/10.1016/j.bmc.2021.116514

Macromolecule Content

Total Structure Weight: 45.41 kDa
Atom Count: 2,858
Modeled Residue Count: 340
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial	A	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5ZP (Subject of Investigation/LOI) Query on 5ZP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(3~{S})-3-[5-(8-cyclopropyl-2-methyl-9~{H}-pyrido[2,3-b]indol-3-yl)-1,3,4-oxadiazol-2-yl]-4-methyl-~{N}-[(1~{R})-1-phenylethyl]pentanamide C₃₁ H₃₃ N₅ O₂ PHZKSLPIUQGPAT-KOSHJBKYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]