7XE3 | pdb_00007xe3

Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)

PDB DOI: https://doi.org/10.2210/pdb7XE3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-03-29 Released: 2022-09-14
Deposition Author(s): Niwa, H., Sato, S., Umehara, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.222 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

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

Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2

Niwa, H., Watanabe, C., Sato, S., Harada, T., Watanabe, H., Tabusa, R., Fukasawa, S., Shiobara, A., Hashimoto, T., Ohno, O., Nakamura, K., Tsuganezawa, K., Tanaka, A., Shirouzu, M., Honma, T., Matsuno, K., Umehara, T.

(2022) ACS Med Chem Lett 13: 1485-1492

DOI: https://doi.org/10.1021/acsmedchemlett.2c00294

Macromolecule Content

Total Structure Weight: 181 kDa
Atom Count: 12,142
Modeled Residue Count: 1,489
Deposited Residue Count: 1,586
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1B	A, B	793	Homo sapiens	Mutation(s): 0 Gene Names: KDM1B, AOF1, C6orf193, LSD2 EC: 1.14.99.66
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB78 (Homo sapiens) Explore Q8NB78 Go to UniProtKB: Q8NB78
PHAROS: Q8NB78 GTEx: ENSG00000165097
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NB78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	F [auth A], N [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
8A2 Query on 8A2 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A]	G [auth A], O [auth B]	3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal C₉ H₇ Br F₂ O JXYLPBJZJRAAJO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain D [auth A]	C [auth A] D [auth A] E [auth A] K [auth B] L [auth B] C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B]	J [auth A], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]