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Crystal structure of chromodomain of CDYL2 in complex with inhibitor UNC3866

Analyse Crystal structure of chromodomain of CDYL2 in complex with inhibitor UNC3866 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V2D
Type: protein
Length: 380 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromodomain Y-like protein 2; UNC3866
UniProt: Q8N8U2
Ligands: 5R0, 5R5, UNX
Pockets: 6 · best druggability 0.46

Structure

x-ray diffraction · 8 distinct chains · 25% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromodomain Y-like protein 2	protein	56	25% helix, 41% strand	Q8N8U2
C	Chromodomain Y-like protein 2	protein	63	22% helix, 38% strand	Q8N8U2
E	Chromodomain Y-like protein 2	protein	57	25% helix, 40% strand	Q8N8U2
G	Chromodomain Y-like protein 2	protein	64	31% helix, 38% strand	Q8N8U2
I	Chromodomain Y-like protein 2	protein	56	25% helix, 41% strand	Q8N8U2
K	Chromodomain Y-like protein 2	protein	55	25% helix, 42% strand	Q8N8U2
J, B, D, F, H	UNC3866	protein	5	0% helix, 40% strand	—
L	UNC3866	protein	4	0% helix, 50% strand	—

Ligands and binding sites

5R0 · 4-~{tert}-butylbenzoic acid · ligand · 6 copies · chains I, K, J, G, L, A, C, B, E, D, F, H
5R5 · Methyl L-serinate · ligand · chains K, L
UNX · Unknown atom or ion · ion · 28 copies · chains A, G, C, E, B, D, K, I, H, L, J

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	176	0.46	0.75	30	5R0, UNX
2	136	0.44	0.76	29	5R0, UNX
3	132	0.40	0.74	23	5R0, UNX
4	101	0.35	0.73	18	5R0
5	88	0.33	0.73	15	5R0

Interfaces

31 interfaces between chains.

G–H · 592 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 574 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 567 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 556 Å² buried · 12 hydrogen bonds · protein-protein
I–J · 550 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 modified, 7 covalent (nonstandard, covalent ligand).

Compared structures

6V2D · Crystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866 · the same entry in another collection · chain H against H, TM-score 1.00

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 Q8N8U2
Elsewhere: RCSB PDB 6V2D · PDBe 6V2D · UniProt Q8N8U2

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