MolNFT v1 · #134686 · protein

Complement factor D inhibited with JH4

5TCC: “Complement factor D inhibited with JH4”. X-ray diffraction, 1 ligand (J56), 8 pockets (best druggability 0.82). MolNFT v1 #134686 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TCC
Type: protein
Length: 1,594 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: J56
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Complement factor D (EC 3.4.21.46)	protein	228	7% helix, 36% strand	P00746
G	Complement factor D (EC 3.4.21.46)	protein	226	8% helix, 36% strand	P00746

Ligands and binding sites

J56 · (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl) acetyl]-1,3-thiazolidine-2-carboxamide · ligand · 9 copies · chains A, C, B, D, E, F, G

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

Pockets

8 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	1147	0.82	0.83	104	J56
2	1101	0.81	0.82	104	J56
3	629	0.74	0.81	55	J56
4	349	0.66	0.80	62	J56
5	130	0.60	0.85	27	empty

Interfaces

8 interfaces between chains.

F–G · 716 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 651 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 487 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 468 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 416 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

5TCC · Complement Factor D inhibited with JH4 · 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 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 P00746
Elsewhere: RCSB PDB 5TCC · PDBe 5TCC · UniProt P00746

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