2W3B

HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND A LIPOPHILIC ANTIFOLATE SELECTIVE FOR MYCOBACTERIUM AVIUM DHFR, 6-((2,5- DIETHOXYPHENYL)AMINOMETHYL)-2,4-DIAMINO-5-METHYLPYRIDO(2,3-D) PYRIMIDINE (SRI-8686)

PDB DOI: https://doi.org/10.2210/pdb2W3B/pdb

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

Deposited: 2008-11-11 Released: 2009-11-17
Deposition Author(s): Leung, A.K.W., Reynolds, R.C., Borhani, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.203
R-Value Work: 0.171
R-Value Observed: 0.172

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structural Basis for Selective Inhibition of Mycobacterium Avium Dihydrofolate Reductase by a Lipophilic Antifolate

Leung, A.K.W., Ross, L.J., Zywno-Van Ginkel, S., Reynolds, R.C., Seitz, L.E., Pathak, V., Barrow, W.W., White, E.L., Suling, W.J., Piper, J.R., Borhani, D.W.

To be published.

Macromolecule Content

Total Structure Weight: 46.15 kDa
Atom Count: 3,848
Modelled Residue Count: 371
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROFOLATE REDUCTASE	A, B	187	Homo sapiens	Mutation(s): 0 EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens) Explore P00374 Go to UniProtKB: P00374
PHAROS: P00374 GTEx: ENSG00000228716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00374
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B]
FOL Query on FOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	FOLIC ACID C₁₉ H₁₉ N₇ O₆ OVBPIULPVIDEAO-LBPRGKRZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B]
VG9 Query on VG9 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	6-{[(2,5-DIETHOXYPHENYL)AMINO]METHYL}-5-METHYLPYRIDO[2,3-D]PYRIMIDINE-2,4-DIAMINE C₁₉ H₂₄ N₆ O₂ KKMWDWUZXFYKLD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
VG9	BindingDB: 2W3B	IC50: min: 0.84, max: 2300 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.203
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.725	α = 90
b = 94.387	β = 90
c = 95.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-17

Deposition Author(s):

Leung, A.K.W.

Reynolds, R.C.

Borhani, D.W.

Revision History (Full details and data files)

Version 1.0: 2009-11-17
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-03-06
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.5: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description