GL1X · GenesisL1 explorer

MolNFT v1 · #163212 · protein

Bicycle toxin conjugate bound to EPHA2

6RW2 · Ephrin type-a receptor 2: “Bicycle toxin conjugate bound to EPHA2”. X-ray diffraction, 1 ligand (29N), 1 pocket (best druggability 0.39). MolNFT v1 #163212 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6RW2
Type
protein
Length
193 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Ephrin type-a receptor 2; Ala-arg-asp-cys-pro-leu-val-asn-pro-leu-cys-leu-his-pro…
EC
2.7.10.1
UniProt
P29317
Ligands
29N
Pockets
1 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 45% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEphrin type-a receptor 2 (EC 2.7.10.1)protein1758% helix, 49% strandP29317
BAla-arg-asp-cys-pro-leu-val-asn-pro-leu-cys-leu-his-pro- gly-TRP-thr-cysprotein1822% helix, 6% strand—

Ligands and binding sites

  • 29N · 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one · ligand · chains A, B
  • GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1880.390.771729N

Interfaces

1 interface between chains.

  • A–B · 960 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

  • 6RW2 · Bicycle Toxin Conjugate bound to EphA2 · the same entry in another collection · chain A against A, TM-score 1.00
  • P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

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