MolNFT v1 · #128110 · protein

Human ERK2 with an ERK1/2 inhibitor

5NGU · Mitogen-activated protein kinase 1: “Human ERK2 with an ERK1/2 inhibitor”. X-ray diffraction, 2 ligands (8X2, SO4), 5 pockets (best druggability 0.69). MolNFT v1 #128110 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NGU
Type: protein
Length: 340 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitogen-activated protein kinase 1
EC: 2.7.11.24
UniProt: P28482
Ligands: 8X2, SO4
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitogen-activated protein kinase 1 (EC 2.7.11.24)	protein	340	38% helix, 16% strand	P28482

Ligands and binding sites

8X2 · 2-[2-[[4-(4-methylpiperazin-1-yl) phenyl]amino]pyrimidin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

5 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	384	0.69	0.81	42	8X2
2	99	0.53	0.83	19	empty
3	93	0.42	0.78	14	empty
4	61	0.30	0.75	13	empty
5	50	0.27	0.74	14	empty

Modifications

Observed in the structure: 1 modified (artifact).

Compared structures

5NGU · Human Erk2 with an Erk1/2 inhibitor · 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 P28482
Elsewhere: RCSB PDB 5NGU · PDBe 5NGU · UniProt P28482

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