8J1K | pdb_00008j1k

co-crystal structure of non-carboxylic acid inhibitor with PHD2

PDB DOI: https://doi.org/10.2210/pdb8J1K/pdb

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

Deposited: 2023-04-13 Released: 2024-04-17
Deposition Author(s): Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Zhang, M., Ding, X., Ren, F., Zhavoronkov, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.308 (Depositor), 0.314 (DCC)
R-Value Work:
0.242 (Depositor), 0.244 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8J1K

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

co-crystal structure of non-carboxylic acid inhibitor with PHD2

Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Man, Z., Ding, X., Ren, F., Zhavoronkov, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.94 kDa
Atom Count: 1,629
Modeled Residue Count: 198
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A	218	Homo sapiens	Mutation(s): 0 Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens) Explore Q9GZT9 Go to UniProtKB: Q9GZT9
PHAROS: Q9GZT9 GTEx: ENSG00000135766
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GZT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SY6 (Subject of Investigation/LOI) Query on SY6 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]	N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide C₂₀ H₁₈ N₆ O₃ ROTOKWNRJPNVEV-CQSZACIVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
SY6	BindingDB: 8J1K	IC50: 2.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.308 (Depositor), 0.314 (DCC)
R-Value Work: 0.242 (Depositor), 0.244 (DCC)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.843	α = 90
b = 80.843	β = 90
c = 63.899	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Zhavoronkov, A.

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.