5NB7: Complement factor D

Complement factor D. Determined by X-ray diffraction at 1.33 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,961
Mol. weight: 25.24 kDa
Ligands: 8NQ
Released: 28 Jun 2017

Explore 5NB7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NB7 contains 10 α-helices and 20 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-48	10	3
β-strand	51-54	4	3
α-helix	56-59	4
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	104-108	5	3
α-helix	111-114	4
β-strand	115	1	5
β-strand	120	1	5
α-helix	122-124	3
β-strand	124A	1	2
α-helix	129A-131	3
β-strand	135-140	6	2
α-helix	150-152	3
β-strand	154	1	4
β-strand	156-163	8	2
α-helix	164	1
α-helix	165-169	5
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-201	4	2
β-strand	208-213	6	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement factor D	A	protein	230	Homo sapiens	P00746 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NB7_1 Complement factor D (chains A)
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSL
SQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPG
TLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCK
GDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASA

Ligands and cofactors

ID	Name	Formula	Copies
8NQ	1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.…	C21 H19 Br N6 O3	1

Water and common crystallization additives (DMS) are not listed.

Primary citation

Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo. Lorthiois, E., Anderson, K., Vulpetti, A. et al. J Med Chem (2017) 60:5717-5735. DOI 10.1021/acs.jmedchem.7b00425 · PubMed

Other PDB entries of the same protein (UniProt P00746 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NAT 1.17 Å, Complement factor D in complex with the inhibitor (S)-Pyrrolidine-1,2-dicarboxylic acid…
2XW9 1.2 Å, Crystal Structure of Complement Factor D mutant S183A
5NAW 1.25 Å, Complement factor D in complex with the inhibitor (1R,3S,5R)-2-Aza-bicyclo[3.1.0]hexane-2…
5MT0 1.29 Å, Complement factor D in complex with a reversible indole carboxylic acid based inhibitor
6FUH 1.37 Å, Complement factor D in complex with the inhibitor (4-((3-(aminomethyl)phenyl)amino)quinaz…
6FUI 1.38 Å, Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H…
5FBE 1.43 Å, Complement factor D in complex with COMPOUND2
5FBI 1.47 Å, Complement factor D in complex with compound 3b
1BIO 1.5 Å, Human complement factor D in complex with isatoic anhydride inhibitor
6FUT 1.5 Å, Complement factor D in complex with the inhibitor (S)-3'-(aminomethyl)-N-(1,2,3,4-tetrahy…
5NAR 1.55 Å, Complement factor D in complex with the inhibitor (S)-pyrrolidine-1,2-dicarboxylic acid…
5MT4 1.65 Å, Complement factor D in complex with a reversible benzoic acid based inhibitor

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