2YJB: Cathepsin L with a nitrile inhibitor

Cathepsin L with a nitrile inhibitor. Determined by X-ray diffraction at 1.4 Å resolution. Released 23 Nov 2011.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 2,013
Mol. weight: 24.85 kDa
Ligands: YJ9
Released: 23 Nov 2011

Explore 2YJB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YJB contains 11 α-helices and 17 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: 11 helices, 17 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
β-strand	23	1	3
α-helix	25-42	18
β-strand	48	1	4
α-helix	50-56	7
α-helix	58-60	3
β-strand	66	1	3
α-helix	70-80	11
β-strand	83-84	2	5
β-strand	85	1	4
α-helix	102-104	3
β-strand	105-107	3	5
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
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

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

>2YJB_1 CATHEPSIN L1 (chains A)
APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ
GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEK
ALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNN
KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV

Ligands and cofactors

ID	Name	Formula	Copies
YJ9	(2S,4R)-4-(2-chlorophenyl)sulfonyl-N-[1-(iminomethyl)cyclopropyl]-1-[1-[4-(trif…	C26 H25 Cl F3 N3 O4 S	1

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

Primary citation

Halogen Bonding at the Active Sites of Human Cathepsin L and Mek1 Kinase: Efficient Interactions in Different Environments. Hardegger, L.A., Kuhn, B., Spinnler, B. et al. ChemMedChem (2011) 6:2048. DOI 10.1002/CMDC.201100353 · 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
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…

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