MolNFT v1 · #177796 · protein

Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with tricyclic small molecule inhibitor jbsnf-000107

7EU5: “Co-crystal structure of human nicotinamide N-methyltransferase (nnmt) with tricyclic small molecule inhibitor…”. X-ray diffraction, 2 ligands (SAH, JDL), 16 pockets (best druggability 0.84). MolNFT v1 #177796 on GenesisL1: 3D…

PDB: 7EU5
Type: protein
Length: 1,023 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinamide N-methyltransferase
EC: 2.1.1.1
UniProt: P40261
Ligands: SAH, JDL
Pockets: 16 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	256	38% helix, 27% strand	P40261
B	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	255	38% helix, 26% strand	P40261
C	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	257	38% helix, 26% strand	P40261
D	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	255	40% helix, 27% strand	P40261

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
JDL · 6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4, 12}]dodeca-4,6,8(12)-trien-11-imine · ligand · 4 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	825	0.84	0.86	99	empty
2	227	0.81	0.94	41	SAH, JDL
3	231	0.80	0.93	44	SAH, JDL
4	148	0.77	0.94	31	SAH
5	143	0.77	0.94	32	SAH

Interfaces

5 interfaces between chains.

A–B · 820 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 704 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 283 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 282 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 239 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7EU5 · Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with tricyclic… · the same entry in another collection · chain B against B, TM-score 1.00
P40261 · AlphaFold monomer V2.0 prediction for nicotinamide N-methyltransferase (P40261) · 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 P40261
Elsewhere: RCSB PDB 7EU5 · PDBe 7EU5 · UniProt P40261

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