6BLF | pdb_00006blf

PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4-(trifluoromethyl)phenyl]ethyl]-1,2,3,4-tetrahydrocarbazol-1-yl]acetic acid

PDB DOI: https://doi.org/10.2210/pdb6BLF/pdb

Classification: Hydrolase/Hydrolase inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-11-10 Released: 2018-11-14
Deposition Author(s): Su, H.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.228 (Depositor), 0.237 (DCC)
R-Value Work:
0.185 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6BLF

Ligand Structure Quality Assessment

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

Literature

Hydrolase complex

Su, H.P.

To be published.

Macromolecule Content

Total Structure Weight: 88.56 kDa
Atom Count: 5,973
Modeled Residue Count: 697
Deposited Residue Count: 746
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent 3',5'-cyclic phosphodiesterase	A, B	373	Homo sapiens	Mutation(s): 0 Gene Names: PDE2A EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for O00408 (Homo sapiens) Explore O00408 Go to UniProtKB: O00408
PHAROS: O00408 GTEx: ENSG00000186642
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00408
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DY1 Query on DY1 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	[(1S)-6-fluoro-8-(methylsulfonyl)-9-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-2,3,4,9-tetrahydro-1H-carbazol-1-yl]acetic acid C₂₄ H₂₃ F₄ N O₄ S KSSMIJUMUAANAX-HIFRSBDPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
DY1	BindingDB: 6BLF	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.228 (Depositor), 0.237 (DCC)
R-Value Work: 0.185 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.03	α = 90
b = 95.83	β = 90
c = 104.13	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-14
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.