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Enah EVH1 in complex with ac-[2-cl-F]-pp-[prom-1]-tedel-NH2

Analyse Enah EVH1 in complex with ac-[2-cl-F]-pp-[prom-1]-tedel-NH2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ND0
Type: protein
Length: 232 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein enabled homolog; 5,6-dihydro-BENZO[H]CINNOLIN-3-ylamine
UniProt: Q8N8S7
Ligands: ACE, 2L5, 8TQ, NO3, SO4
Pockets: 3 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein enabled homolog	protein	109	21% helix, 48% strand	Q8N8S7
C, F	5,6-dihydro-BENZO[H]CINNOLIN-3-ylamine	protein	7	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, F
2L5 · 2-chloro-L-phenylalanine · ligand · 2 copies · chains A, C, B, F
8TQ · (3~{S},7~{R},10~{R},13~{S})-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carbaldehyde · ligand · 2 copies · chains A, C, B, F
NO3 · Nitrate ion · ion · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.35	0.75	22	empty
2	59	0.28	0.74	12	SO4
3	51	0.27	0.75	10	SO4

Interfaces

3 interfaces between chains.

A–B · 385 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 331 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 329 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

5ND0 · ENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-1]-TEDEL-NH2 · the same entry in another collection · chain A against A, TM-score 1.00
Q8N8S7 · AlphaFold monomer V2.0 prediction for protein enabled homolog (Q8N8S7) · a predicted model of the same protein · chain B 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 Q8N8S7
Elsewhere: RCSB PDB 5ND0 · PDBe 5ND0 · UniProt Q8N8S7

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