7XE1 | pdb_00007xe1

Crystal structure of LSD2 in complex with cis-4-Br-PCPA

PDB DOI: https://doi.org/10.2210/pdb7XE1/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: 2.07 Å
R-Value Free:
0.192 (Depositor), 0.191 (DCC)
R-Value Work:
0.164 (Depositor), 0.163 (DCC)
R-Value Observed:
0.166 (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: 182.06 kDa
Atom Count: 13,150
Modeled Residue Count: 1,491
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 7 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 V [auth B] MOL2 format, chain F [auth A] MOL2 format, chain V [auth B] mmCIF format, chain F [auth A] mmCIF format, chain V [auth B]	F [auth A], V [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain V [auth B]
DIJ Query on DIJ Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth B] mmCIF format, chain G [auth A]	G [auth A], W [auth B]	3-(4-bromophenyl)propanal C₉ H₉ Br O RXZJWVPNFPPSEM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain W [auth B]
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]
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] J [auth A] K [auth A] L [auth A] AA [auth B], BA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] S [auth B] T [auth B] C [auth A], D [auth A], E [auth A], S [auth B], T [auth B], U [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 S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]