MolNFT v1 · #144218 · protein

Influenza a M2 transmembrane domain bound to a spiroadamantane inhibitor

6BMZ · Matrix protein 2: “Influenza a M2 transmembrane domain bound to a spiroadamantane inhibitor”. X-ray diffraction, 3 ligands (E01, NH2, CL), 9 pockets (best druggability 0.83). MolNFT v1 #144218 on GenesisL1: 3D structure, binding…

PDB: 6BMZ
Type: protein
Length: 382 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Matrix protein 2
UniProt: Q20MD5
Ligands: E01, NH2, CL
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 88% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, H, I, K, L, M, O, P	Matrix protein 2	protein	24	88% helix, 0% strand	Q20MD5
B, D, F, J	Matrix protein 2	protein	23	91% helix, 0% strand	Q20MD5
G, N	Matrix protein 2	protein	25	84% helix, 0% strand	Q20MD5

Ligands and binding sites

E01 · (1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine · ligand · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
NH2 · Amino group · ion · 16 copies · chains A, B, C, I, D, E, F, G, H, J, K, L, M, N, O, P
CL · Chloride ion · ion · 4 copies · chains A, B, C, D, F, G, I, J, K, L, O, P

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	175	0.83	0.98	30	E01
2	198	0.83	0.97	32	E01
3	192	0.82	0.96	30	E01
4	178	0.81	0.96	30	E01
5	738	0.68	0.75	50	empty

Interfaces

34 interfaces between chains.

M–N · 536 Å² buried · 2 hydrogen bonds · protein-protein
G–H · 509 Å² buried · 1 hydrogen bond · protein-protein
N–O · 507 Å² buried · 3 hydrogen bonds · protein-protein
M–P · 498 Å² buried · 3 hydrogen bonds · protein-protein
I–L · 497 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6BMZ · Influenza A M2 transmembrane domain bound to a spiroadamantane inhibitor · 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 Q20MD5
Elsewhere: RCSB PDB 6BMZ · PDBe 6BMZ · UniProt Q20MD5

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