8PC4

MEMBRANE TARGET COMPLEX 1

PDB DOI: https://doi.org/10.2210/pdb8PC4/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2023-06-09 Released: 2024-06-26
Deposition Author(s): Garau, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.301 (Depositor), 0.300 (DCC)
R-Value Work:
0.265 (Depositor), 0.260 (DCC)
R-Value Observed:
0.267 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

NAPE-PLD is target of thiazide diuretics

Chiarugi, S., Margheriti, F., De Lorenzi, V., Martino, E., Margheritis, E.G., Moscardini, A., Marotta, R., Chaves-Sanjuan, A., Del Seppia, C., Federighi, G., Lapi, D., Bandiera, T., Rapposelli, S., Scuri, R., Bolognesi, M., Garau, G.

(2025) Cell Chem Biol

DOI: https://doi.org/10.1016/j.chembiol.2025.01.008

Macromolecule Content

Total Structure Weight: 97.29 kDa
Atom Count: 5,928
Modelled Residue Count: 666
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D	A, B	393	Homo sapiens	Mutation(s): 0 Gene Names: NAPEPLD, C7orf18 EC: 3.1.4.54
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IQ20 (Homo sapiens) Explore Q6IQ20 Go to UniProtKB: Q6IQ20
PHAROS: Q6IQ20 GTEx: ENSG00000161048
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IQ20
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE (Subject of Investigation/LOI) Query on 3PE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B]	E [auth A], P [auth B]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain P [auth B]
DXC (Subject of Investigation/LOI) Query on DXC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], Q [auth B], R [auth B]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C₂₄ H₄₀ O₄ KXGVEGMKQFWNSR-LLQZFEROSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth B] Focus chain R [auth B]
HCZ (Subject of Investigation/LOI) Query on HCZ Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	6-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide 1,1-dioxide C₇ H₈ Cl N₃ O₄ S₂ JZUFKLXOESDKRF-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	C [auth A], D [auth A], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B]