6YVT | pdb_00006yvt

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 (Depositor), 0.270 (DCC)
R-Value Work:
0.237 (Depositor), 0.240 (DCC)
R-Value Observed:
0.238 (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

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

Organizational Affiliation

Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK.

Macromolecule Content

Total Structure Weight: 171.21 kDa
Atom Count: 9,358
Modeled Residue Count: 1,182
Deposited Residue Count: 1,512
Unique protein chains: 1

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 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 GTEx: ENSG00000135766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZT9
Sequence Annotations 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] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF 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		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain T [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E] mmCIF format, chain R [auth E]	R [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain R [auth E] Interactions & Density Focus chain R [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth E] MOL2 format, chain Q [auth E] mmCIF format, chain Q [auth E]	Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth E] Interactions & Density Focus chain Q [auth E]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF 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		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain S [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.266 (Depositor), 0.270 (DCC)
R-Value Work: 0.237 (Depositor), 0.240 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.456	α = 90
b = 103.018	β = 90
c = 196.028	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

Chowdhury, R.

Demetriades, M.

Schofield, C.J.

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description