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Crystal structure of mouse CRY1 in complex with KL001 compound

Analyse Crystal structure of mouse CRY1 in complex with KL001 compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DLI
Type: protein
Length: 1,423 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cryptochrome-1
UniProt: P97784
Ligands: H8X
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cryptochrome-1	protein	472	50% helix, 7% strand	P97784
B	Cryptochrome-1	protein	475	51% helix, 7% strand	P97784
C	Cryptochrome-1	protein	476	51% helix, 8% strand	P97784

Ligands and binding sites

H8X · N-[(2R)-3-carbazol-9-yl-2-oxidanyl-propyl]-N-(furan-2-ylmethyl)methanesulfonamide · ligand · 3 copies · chains A, C, B
EDO · 1,2-ethanediol · additive · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	865	0.83	0.85	80	H8X
2	539	0.77	0.84	54	H8X
3	509	0.77	0.84	57	empty
4	879	0.72	0.77	69	empty
5	353	0.72	0.84	38	H8X

Interfaces

3 interfaces between chains.

A–C · 794 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 451 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 395 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7DLI · Crystal structure of mouse CRY1 in complex with KL001 compound · the same entry in another collection · chain A against A, TM-score 1.00
P97784 · AlphaFold monomer V2.0 prediction for cryptochrome-1 (P97784) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P97784
Elsewhere: RCSB PDB 7DLI · PDBe 7DLI · UniProt P97784

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