7O9Z | pdb_00007o9z

Crystal structure of Human Menin in complex with BD-08

PDB DOI: https://doi.org/10.2210/pdb7O9Z/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-18 Released: 2022-07-27
Deposition Author(s): Groves, M.R., Gao, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.243 (Depositor), 0.240 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (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

Crystal structure of Human Menin in complex with BD-08

Groves, M.R., Gao, K.

To be published.

Macromolecule Content

Total Structure Weight: 55.53 kDa
Atom Count: 3,875
Modeled Residue Count: 462
Deposited Residue Count: 494
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	494	Homo sapiens	Mutation(s): 0 Gene Names: MEN1, hCG_2017452
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V6N (Subject of Investigation/LOI) Query on V6N 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]	(~{E})-2-cyano-3-(2~{H}-indazol-6-yl)-~{N}-(2-morpholin-4-ylethyl)prop-2-enamide C₁₇ H₁₉ N₅ O₂ DCPLXQDYVXXNNX-OQLLNIDSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A]