MolNFT v1 · #122081 · protein

Structure of CDL2.2, a computationally designed vitamin-D3 binder

5IEN: “Structure of CDL2.2, a computationally designed vitamin-D3 binder”. X-ray diffraction, 1 ligand (VDY), 2 pockets (best druggability 0.74). MolNFT v1 #122081 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IEN
Type: protein
Length: 253 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CDL2.2
Ligands: VDY
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CDL2.2	protein	129	28% helix, 47% strand	—
B	CDL2.2	protein	124	29% helix, 49% strand	—

Ligands and binding sites

VDY · 3-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexanol · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	370	0.74	0.85	42	VDY
2	304	0.72	0.85	36	VDY

Interfaces

1 interface between chains.

A–B · 1120 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5IEN · Structure of CDL2.2, a computationally designed Vitamin-D3 binder · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 5IEN · PDBe 5IEN

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