MolNFT v1 · #115624 · protein

The structure of the NK1 fragment of HGF/SF complexed with MB605

5CP9 · Hepatocyte growth factor: “The structure of the NK1 fragment of HGF/SF complexed with MB605”. X-ray diffraction, 1 ligand (6O5), 3 pockets (best druggability 0.69). MolNFT v1 #115624 on GenesisL1: 3D structure, binding sites and…

PDB: 5CP9
Type: protein
Length: 346 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatocyte growth factor
UniProt: P14210
Ligands: 6O5
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hepatocyte growth factor	protein	173	11% helix, 31% strand	P14210
B	Hepatocyte growth factor	protein	173	12% helix, 29% strand	P14210

Ligands and binding sites

6O5 · 3-(furan-2-yl)propanoic acid · ligand · chains B
EDO · 1,2-ethanediol · additive · chains B

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

Pockets

3 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	477	0.69	0.80	55	empty
2	265	0.53	0.76	49	empty
3	99	0.38	0.76	21	empty

Interfaces

1 interface between chains.

A–B · 1246 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5CP9 · The structure of the NK1 fragment of HGF/SF complexed with MB605 · the same entry in another collection · chain A against A, TM-score 1.00
P14210 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (P14210) · a predicted model of the same protein · chain A against A, TM-score 0.60

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 P14210
Elsewhere: RCSB PDB 5CP9 · PDBe 5CP9 · UniProt P14210

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