5MQY: CATHEPSIN L

CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile. Determined by X-ray diffraction at 1.13 Å resolution. Released 22 Mar 2017.

Method: X-ray diffraction
Resolution: 1.13 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,009
Mol. weight: 25.08 kDa
Ligands: GH4
Released: 22 Mar 2017

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

Secondary structure: helices and β-sheets

5MQY contains 12 α-helices and 15 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: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	2
α-helix	25-42	18
β-strand	48	1	3
α-helix	50-56	7
α-helix	58-60	3
α-helix	64-66	3
α-helix	70-80	11
β-strand	83-84	2	4
β-strand	85	1	3
α-helix	102-104	3
β-strand	105-107	3	4
β-strand	111-114	4	1
α-helix	115-116	2
α-helix	119-129	11
β-strand	132-136	5	1
α-helix	141-144	4
β-strand	150-151	2	1
β-strand	163-172	10	1
β-strand	181-186	6	1
β-strand	189	1	2
β-strand	195	1	1
β-strand	198-202	5	1
α-helix	208-210	3
β-strand	216-219	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cathepsin L1	A	protein	220	Homo sapiens	P07711 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MQY_1 Cathepsin L1 (chains A)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNN
KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
GH4	4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbon…	C21 H19 F N4 O3	1

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

Primary citation

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors. Kuhn, B., Tichy, M., Wang, L. et al. J Med Chem (2017) 60:2485-2497. DOI 10.1021/acs.jmedchem.6b01881 · PubMed

Other PDB entries of the same protein (UniProt P07711 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XU3 0.9 Å, Cathepsin L with a nitrile inhibitor
5MAE 1.0 Å, CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro…
5MAJ 1.0 Å, CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morp…
2XU4 1.12 Å, Cathepsin L with a nitrile inhibitor
2YJC 1.14 Å, Cathepsin L with a nitrile inhibitor
2YJ2 1.15 Å, Cathepsin L with a nitrile inhibitor
3HHA 1.27 Å, Crystal structure of cathepsin L in complex with AZ12878478
2YJ8 1.3 Å, Cathepsin L with a nitrile inhibitor
2YJ9 1.35 Å, Cathepsin L with a nitrile inhibitor
7Z58 1.35 Å, Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin
6EZP 1.37 Å, CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-12,17-dioxa-4…
2YJB 1.4 Å, Cathepsin L with a nitrile inhibitor

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