6YVT

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253

PDB DOI: https://doi.org/10.2210/pdb6YVT/pdb

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

Deposited: 2020-04-28 Released: 2020-05-20
Deposition Author(s): Chowdhury, R., Demetriades, M., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.266
R-Value Work: 0.237
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Dynamic combinatorial chemistry employing boronic acids/boronate esters leads to potent oxygenase inhibitors.

Demetriades, M., Leung, I.K., Chowdhury, R., Chan, M.C., McDonough, M.A., Yeoh, K.K., Tian, Y.M., Claridge, T.D., Ratcliffe, P.J., Woon, E.C., Schofield, C.J.

(2012) Angew Chem Int Ed Engl 51: 6672-6675

PubMed: 22639232 Search on PubMed
DOI: https://doi.org/10.1002/anie.201202000
Primary Citation of Related Structures:
6YVT

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egl nine homolog 1	A, B, C, D, E, F A, B, C, D, E, F	252	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZT9
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PW2 (Subject of Investigation/LOI) Query on PW2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain T [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain T [auth F]	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], T [auth F]	2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid C₁₉ H₁₆ N₂ O₅ PJNFXXUNCQIGBZ-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E]	R [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth E] MOL2 format, chain Q [auth E]	Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain S [auth F] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain S [auth F]	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], S [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Ligand Interaction