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Complement factor D inhibited with JH3

Analyse Complement factor D inhibited with JH3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TCA
Type: protein
Length: 1,596 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement factor D
EC: 3.4.21.46
UniProt: P00746
Ligands: J55
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Complement factor D (EC 3.4.21.46)	protein	228	8% helix, 36% strand	P00746

Ligands and binding sites

J55 · 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide · ligand · 9 copies · chains A, C, B, D, F, E, G

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.84	0.85	106	J55
2	870	0.83	0.85	95	J55
3	622	0.78	0.83	61	J55
4	168	0.68	0.87	34	empty
5	97	0.64	0.90	28	empty

Interfaces

7 interfaces between chains.

A–B · 691 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 600 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 512 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 482 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 473 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

5TCA · Complement Factor D inhibited with JH3 · the same entry in another collection · chain G against G, TM-score 1.00
P00746 · AlphaFold monomer V2.0 prediction for complement factor D (P00746) · 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 P00746
Elsewhere: RCSB PDB 5TCA · PDBe 5TCA · UniProt P00746

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