MolNFT v1 · #161709 · protein

Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1- amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-YL)METHOXY)PHENYL)ACETIC acid

6QMR: “Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1…”. X-ray diffraction, 1 ligand (J6T), 16 pockets (best druggability 0.81). MolNFT v1 #161709 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QMR
Type: protein
Length: 1,373 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement factor D
EC: 3.4.21.46
UniProt: P00746
Ligands: J6T
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement factor D (EC 3.4.21.46)	protein	230	9% helix, 36% strand	P00746
B, C, D, E	Complement factor D (EC 3.4.21.46)	protein	229	9% helix, 36% strand	P00746
F	Complement factor D (EC 3.4.21.46)	protein	227	8% helix, 36% strand	P00746

Ligands and binding sites

J6T · 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	893	0.81	0.83	107	empty
2	1054	0.76	0.78	120	empty
3	663	0.74	0.80	78	empty
4	402	0.70	0.82	58	empty
5	314	0.58	0.77	38	empty

Interfaces

10 interfaces between chains.

A–F · 660 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 654 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 502 Å² buried · 2 hydrogen bonds · protein-protein
D–F · 481 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 466 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

6QMR · Complement factor D in complex with the inhibitor… · the same entry in another collection · chain F against F, TM-score 1.00
P00746 · AlphaFold monomer V2.0 prediction for complement factor D (P00746) · a predicted model of the same protein · chain F 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 6QMR · PDBe 6QMR · UniProt P00746

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