7OCB | pdb_00007ocb

Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B

PDB DOI: https://doi.org/10.2210/pdb7OCB/pdb

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

Deposited: 2021-04-26 Released: 2022-05-04
Deposition Author(s): Johansson, C., Krojer, T., Park, K., Xiong, Y., Jin, J., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.206 (Depositor), 0.208 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.181 (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 Spindlin1 in complex with the inhibitor XY49-92B

Johansson, C., Krojer, T., Park, K., Xiong, Y., Jin, J., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 26.55 kDa
Atom Count: 1,837
Modeled Residue Count: 196
Deposited Residue Count: 222
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spindlin-1	A [auth B]	222	Homo sapiens	Mutation(s): 0 Gene Names: SPIN1, OCR, SPIN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y657 (Homo sapiens) Explore Q9Y657 Go to UniProtKB: Q9Y657
PHAROS: Q9Y657 GTEx: ENSG00000106723
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y657
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V88 (Subject of Investigation/LOI) Query on V88 Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-2N-[2-(dimethylamino)ethyl]-6-methoxy-4N-(1-propan-2-ylpiperidin-4-yl)quinazoline-2,4-diamine C₃₂ H₄₇ N₇ O₂ CHEFNBAYIGSOIR-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]