MolNFT v1 · #115764 · protein

Humanized yeast acc carboxyltransferase domain bound to 6,7-dimethyl- 1'-[(7-methyl-1H-indazol-5-YL)CARBONYL]SPIRO[CHROMENE-2,4'- piperidin]-4(3H)-one

5CTB · Acetyl-CoA carboxylase: “Humanized yeast acc carboxyltransferase domain bound to 6,7-dimethyl…”. X-ray diffraction, 2 ligands (57J, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #115764 on GenesisL1: 3D structure, binding…

PDB: 5CTB
Type: protein
Length: 2,040 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetyl-CoA carboxylase
EC: 6.4.1.2, 6.3.4.14
UniProt: Q00955
Ligands: 57J, SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14)	protein	695	41% helix, 20% strand	Q00955
B	Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14)	protein	673	40% helix, 21% strand	Q00955
C	Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14)	protein	672	42% helix, 21% strand	Q00955

Ligands and binding sites

57J · 6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl) carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 5 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	975	0.85	0.86	102	57J
2	496	0.76	0.84	32	empty
3	330	0.75	0.86	41	57J
4	531	0.71	0.80	33	empty
5	245	0.64	0.82	40	empty

Interfaces

2 interfaces between chains.

B–C · 5565 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 1395 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5CTB · Humanized yeast ACC carboxyltransferase domain bound to… · the same entry in another collection · chain A against A, TM-score 1.00
Q00955 · AlphaFold monomer V2.0 prediction for acetyl-CoA carboxylase (Q00955) · a predicted model of the same protein · chain C 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 Q00955
Elsewhere: RCSB PDB 5CTB · PDBe 5CTB · UniProt Q00955

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