MolNFT v1 · #119880 · protein

Crystal structure of vdr in complex with dlam-2P

5GIC · Vitamin D3 receptor: “Crystal structure of vdr in complex with dlam-2P”. X-ray diffraction, 1 ligand (DLC), 3 pockets (best druggability 0.85). MolNFT v1 #119880 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GIC
Type: protein
Length: 247 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor; SRC1
UniProt: P13053
Ligands: DLC
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor	protein	237	65% helix, 3% strand	P13053
C	SRC1	protein	10	70% helix, 0% strand	—

Ligands and binding sites

DLC · (3~{R},5~{S})-5-[(2~{R})-2-[(1~{R},3~{a}~{S},4~{Z},7~{a}~{R})-7~{a}-methyl-4-[(2~{E})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(2-phenylethyl)pyrrolidin-2-one · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	550	0.85	0.90	48	DLC
2	85	0.34	0.75	16	empty
3	56	0.31	0.76	10	empty

Interfaces

1 interface between chains.

A–C · 495 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5GIC · Crystal structure of VDR in complex with DLAM-2P · 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
Every structure of UniProt P13053
Elsewhere: RCSB PDB 5GIC · PDBe 5GIC · UniProt P13053

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