MolNFT v1 · #120999 · protein

Binding site elucidation and structure guided design of macrocyclic il-17A antagonists

5HI4 · Interleukin-17A: “Binding site elucidation and structure guided design of macrocyclic il-17A antagonists”. X-ray diffraction, 1 ligand (63P), 13 pockets (best druggability 0.76). MolNFT v1 #120999 on GenesisL1: 3D structure, binding…

PDB: 5HI4
Type: protein
Length: 1,060 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-17A; Cat-2000 Fab heavy chain; Cat-2000 Fab light chain; Synthetic il-17A…
UniProt: Q16552
Ligands: 63P
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-17A	protein	89	4% helix, 57% strand	Q16552
B	Interleukin-17A	protein	91	4% helix, 55% strand	Q16552
C, H	Cat-2000 Fab heavy chain	protein	220	8% helix, 52% strand	—
D, L	Cat-2000 Fab light chain	protein	213	8% helix, 50% strand	—
I	Synthetic il-17A peptide inhibitor	protein	14	50% helix, 21% strand	—

Ligands and binding sites

63P · (9'S,17'R)-6'-chloro-N-methyl-9'-{[(1-methyl-1H-pyrazol-5-yl)carbonyl]amino}-10',19'-dioxo-2'-oxa-11', 18'-diazaspiro[cyclopentane-1,21'-tetracyclo[20.2.2.2~12,15~.1~3,7~]nonacosane]-1'(24'), 3'(29'),4',6',12',14',22',25',27'-nonaene-17'-carboxamide · ligand · chains A, B

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

Pockets

13 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	976	0.76	0.78	78	63P
2	224	0.62	0.82	41	empty
3	448	0.58	0.74	52	empty
4	141	0.56	0.82	35	empty
5	393	0.56	0.74	48	empty

Interfaces

11 interfaces between chains.

H–L · 1819 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1799 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1091 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 361 Å² buried · 3 hydrogen bonds · protein-protein
A–L · 358 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5HI4 · Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists · the same entry in another collection · chain I against I, TM-score 1.00
Q16552 · AlphaFold monomer V2.0 prediction for interleukin-17A (Q16552) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q16552
Elsewhere: RCSB PDB 5HI4 · PDBe 5HI4 · UniProt Q16552

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