MolNFT v1 · #124694 · protein

Trka jm-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2- PYRIDYL)UREA

5KMO · High affinity nerve growth factor receptor: “Trka jm-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2- PYRIDYL)UREA”. X-ray diffraction, 1 ligand (6UM), 2 pockets (best druggability 0.72). MolNFT v1 #124694 on GenesisL1: 3D…

PDB: 5KMO
Type: protein
Length: 291 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: High affinity nerve growth factor receptor
EC: 2.7.10.1
UniProt: P04629
Ligands: 6UM
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	High affinity nerve growth factor receptor (EC 2.7.10.1)	protein	291	38% helix, 17% strand	P04629

Ligands and binding sites

6UM · 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea · ligand · chains A

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

Pockets

2 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	546	0.72	0.80	53	6UM
2	53	0.27	0.73	14	empty

Compared structures

5KMO · TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2-pyridyl)urea · the same entry in another collection · chain A against A, TM-score 1.00
P04629 · AlphaFold monomer V2.0 prediction for high affinity nerve growth factor receptor (P04629) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P04629
Elsewhere: RCSB PDB 5KMO · PDBe 5KMO · UniProt P04629

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