3HHA: Cathepsin L

Crystal structure of cathepsin L in complex with AZ12878478. Determined by X-ray diffraction at 1.27 Å resolution. Released 23 Jun 2009.

Method: X-ray diffraction
Resolution: 1.27 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,109
Mol. weight: 98.68 kDa
Ligands: NOW
Released: 23 Jun 2009

Explore 3HHA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HHA contains 49 α-helices and 60 β-strands across 4 chains. 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: 13 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	112-114	3	1
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	1
α-helix	141-144	4
β-strand	150-151	2	1
β-strand	163-172	10	1
α-helix	176-178	3
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	216-218	3	1

Chains B and D: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	5
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	6
α-helix	25-42	18
β-strand	48	1	7
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	8
β-strand	85	1	7
α-helix	102-104	3
β-strand	105-107	3	8
β-strand	112-114	3	5
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	5
α-helix	141-144	4
β-strand	150-151	2	5
β-strand	163-172	10	5
β-strand	181-186	6	5
β-strand	189	1	6
β-strand	195	1	5
β-strand	198-202	5	5
α-helix	208-210	3
β-strand	216-218	3	5

Chain C: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	9
α-helix	7-10	4
α-helix	14-16	3
β-strand	18	1	10
α-helix	25-42	18
β-strand	48	1	11
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	12
β-strand	85	1	11
α-helix	102-104	3
β-strand	105-107	3	12
β-strand	112-114	3	9
α-helix	115-116	2
α-helix	119-128	10
β-strand	132-136	5	9
α-helix	141-144	4
β-strand	150-151	2	9
β-strand	163-171	9	9
β-strand	182-186	5	9
β-strand	189	1	10
β-strand	195	1	9
β-strand	198-202	5	9
α-helix	208-210	3
β-strand	216-218	3	9

Molecules and chains

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

Sequence of entity 1 (A, B, C, D), FASTA

>3HHA_1 Cathepsin L1 (chains A, B, C, D)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDAGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNN
KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
NOW	Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2Z)-2-iminoethyl]-…	C21 H29 N5 O2	4

Water and common crystallization additives (GOL, PGE, ACT, PG4) are not listed.

Primary citation

Dipeptidyl nitrile inhibitors of Cathepsin L. Asaad, N., Bethel, P.A., Coulson, M.D. et al. Bioorg Med Chem Lett (2009) 19:4280-4283. DOI 10.1016/j.bmcl.2009.05.071 · 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
5MQY 1.13 Å, CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluorop…
2YJC 1.14 Å, Cathepsin L with a nitrile inhibitor
2YJ2 1.15 Å, Cathepsin L with a nitrile inhibitor
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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