MolNFT v1 · #159538 · protein

Crystal structure analysis of PIP4K2A

6OSP · Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha: “Crystal structure analysis of PIP4K2A”. X-ray diffraction, 1 ligand (N51), 6 pockets (best druggability 0.68). MolNFT v1 #159538 on GenesisL1: 3D structure, binding sites and…

PDB: 6OSP
Type: protein
Length: 630 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
EC: 2.7.1.149
UniProt: P48426
Ligands: N51
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149)	protein	320	38% helix, 23% strand	P48426
B	Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149)	protein	310	36% helix, 23% strand	P48426

Ligands and binding sites

N51 · 4-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}-N-(3-{[6-(1H-indol-3-yl)pyrimidin-4-yl]amino}phenyl)benzamide · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

6 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	470	0.68	0.79	41	N51
2	414	0.67	0.79	47	N51
3	103	0.41	0.77	19	GOL
4	98	0.38	0.76	23	GOL
5	76	0.33	0.75	25	empty

Interfaces

1 interface between chains.

A–B · 1489 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6OSP · Crystal Structure Analysis of PIP4K2A · the same entry in another collection · chain A against A, TM-score 1.00
P48426 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 5-phosphate 4-kinase type-2… · a predicted model of the same protein · chain B 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 P48426
Elsewhere: RCSB PDB 6OSP · PDBe 6OSP · UniProt P48426

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