8VA6

Menin in complex with Ziftomenib (KO-539)

PDB DOI: https://doi.org/10.2210/pdb8VA6/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-11 Released: 2024-11-20
Deposition Author(s): Clegg, B.D., Linhares, B.M., Cierpicki, T., Grembecka, J.
Funding Organization(s): Leukemia & Lymphoma Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.193
R-Value Work: 0.158

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Menin in complex with Ziftomenib (KO-539)

Clegg, B.D., Linhares, B.M., Cierpicki, T., Grembecka, J.

To be published.

Macromolecule Content

Total Structure Weight: 56.43 kDa
Atom Count: 4,245
Modelled Residue Count: 468
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menin	A	489	Homo sapiens	Mutation(s): 0 Gene Names: MEN1, SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens) Explore O00255 Go to UniProtKB: O00255
PHAROS: O00255 GTEx: ENSG00000133895
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K5O (Subject of Investigation/LOI) Query on K5O 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]	Ziftomenib C₃₃ H₄₂ F₃ N₉ O₂ S₂ BGGALFIXXQOTPY-NRFANRHFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A]	G [auth A], I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A]	E [auth A], H [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A]	F [auth A], K [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain K [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]