4NPV | pdb_00004npv

Crystal structure of human PDE1B bound to inhibitor 7A (6,7,8-trimethoxy-N-(pentan-3-yl)quinazolin-4-amine)

PDB DOI: https://doi.org/10.2210/pdb4NPV/pdb

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

Deposited: 2013-11-22 Released: 2014-07-16
Deposition Author(s): Pandit, J., Evdomikov, A., Mansour, M., Simons, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.205 (Depositor), 0.203 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4NPV

Ligand Structure Quality Assessment

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

Literature

Small-molecule phosphodiesterase probes: discovery of potent and selective CNS-penetrable quinazoline inhibitors of PDE1

Humphrey, J.M., Yang, E.X., Am Ende, C.W., Arnold, E.P., Head, J.L., Jenkinsonb, S., Lebel, L.A., Liras, S., Pandit, J., Samas, B., Vajdos, F., Simons, S.P., Evdokimova, A., Mansour, M., Menniti, F.S.

(2014) Medchemcomm

DOI: https://doi.org/10.1039/C4MD00113C

Macromolecule Content

Total Structure Weight: 42.53 kDa
Atom Count: 2,805
Modeled Residue Count: 323
Deposited Residue Count: 369
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B	A	369	Homo sapiens	Mutation(s): 0 Gene Names: PDE1B, PDE1B1, PDES1B EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q01064 (Homo sapiens) Explore Q01064 Go to UniProtKB: Q01064
PHAROS: Q01064 GTEx: ENSG00000123360
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01064
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0NK Query on 0NK 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]	6,7,8-trimethoxy-N-(pentan-3-yl)quinazolin-4-amine C₁₆ H₂₃ N₃ O₃ TVJPHOZGPOLRKC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
0NK	BindingDB: 4NPV	IC50: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.205 (Depositor), 0.203 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.416	α = 90
b = 88.416	β = 90
c = 134.973	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations