8HDG

Small peptide enhances the binding of nutline-3a to MdmX

PDB DOI: https://doi.org/10.2210/pdb8HDG/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia
Mutation(s): No

Deposited: 2022-11-04 Released: 2022-11-30
Deposition Author(s): Cheng, X.Y., Huang, Y., Wei, Q.Y., Huang, J.J., Peng, Y.W., Su, Z.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.241
R-Value Work: 0.204

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Small peptide enhances the binding of nutline-3a to MdmX

Cheng, X.Y., Huang, Y., Wei, Q.Y., Huang, J.J., Peng, Y.W., Su, Z.D.

To be published.

Macromolecule Content

Total Structure Weight: 54.32 kDa
Atom Count: 3,483
Modelled Residue Count: 392
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein DKFZp686B01123	A [auth D], B [auth A], C, D [auth B]	111	Homo sapiens	Mutation(s): 0 Gene Names: DKFZp686B01123
UniProt & NIH Common Fund Data Resources
Find proteins for O15151 (Homo sapiens) Explore O15151 Go to UniProtKB: O15151
PHAROS: O15151 GTEx: ENSG00000198625
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15151
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NUT (Subject of Investigation/LOI) Query on NUT Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain J [auth B] MOL2 format, chain E [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth B] mmCIF format, chain E [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth B]	E [auth D], G [auth A], I [auth C], J [auth B]	4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one C₃₀ H₃₀ Cl₂ N₄ O₄ BDUHCSBCVGXTJM-WUFINQPMSA-N		Interactions Focus chain E [auth D] Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth B] Interactions & Density Focus chain E [auth D] Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth B]
O4B Query on O4B Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth D], H [auth A], K [auth B], L [auth B]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth D] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB: 8HDG	Ki: min: 1599, max: 6.90e+4 (nM) from 2 assay(s)
NUT	BindingDB: 8HDG	IC50: min: 4300, max: 1.00e+4 (nM) from 2 assay(s)