8GSJ | pdb_00008gsj

APC-Asef tripeptide inhibitor

PDB DOI: https://doi.org/10.2210/pdb8GSJ/pdb

Classification: PROTEIN BINDING/INHIBITOR
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-09-06 Released: 2023-12-27
Deposition Author(s): Zhang, J., Wang, X.F., Song, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.256 (Depositor), 0.266 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.201 (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

APC-Asef tripeptide inhibitor

Zhang, J., Wang, X.F., Song, K.

To be published.

Macromolecule Content

Total Structure Weight: 38.75 kDa
Atom Count: 2,786
Modeled Residue Count: 336
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenomatous polyposis coli protein	A	336	Homo sapiens	Mutation(s): 0 Gene Names: APC
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054 Go to UniProtKB: P25054
PHAROS: P25054 GTEx: ENSG00000134982
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25054
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAL (Subject of Investigation/LOI) Query on NAL 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]	BETA-(2-NAPHTHYL)-ALANINE C₁₃ H₁₃ N O₂ JPZXHKDZASGCLU-LBPRGKRZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K8C (Subject of Investigation/LOI) Query on K8C 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]	2-methylsulfanylpyrimidine-4-carbaldehyde C₆ H₆ N₂ O S QGJXHPACBLAFFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GLU Query on GLU 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]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GJZ (Subject of Investigation/LOI) Query on GJZ Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(1R,2S)-2-phenylcyclopropanamine C₉ H₁₁ N AELCINSCMGFISI-DTWKUNHWSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
LEU Query on LEU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [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] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]