MolNFT v1 · #103319 · protein

Crystal structure of vccnt-7C8C bound to gemcitabine

4PD5 · Nupc family protein: “Crystal structure of vccnt-7C8C bound to gemcitabine”. X-ray diffraction, 2 ligands (GEO, NA), 6 pockets (best druggability 0.64). MolNFT v1 #103319 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PD5
Type: protein
Length: 403 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nupc family protein
UniProt: Q9KPL5
Ligands: GEO, NA
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nupc family protein	protein	403	77% helix, 0% strand	Q9KPL5

Ligands and binding sites

GEO · Gemcitabine · ligand · chains A
NA · Sodium ion · metal · chains A
DMU · Decyl-beta-D-maltopyranoside · additive · chains A

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	380	0.64	0.79	37	GEO
2	165	0.58	0.81	21	empty
3	121	0.43	0.76	18	empty
4	67	0.30	0.73	17	empty
5	57	0.28	0.73	14	empty

Compared structures

4PD5 · Crystal structure of vcCNT-7C8C bound to gemcitabine · 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 Q9KPL5
Elsewhere: RCSB PDB 4PD5 · PDBe 4PD5 · UniProt Q9KPL5

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