2CN0: Prothrombin precursor

Complex of Recombinant Human Thrombin with a Designed Inhibitor. Determined by X-ray diffraction at 1.3 Å resolution. Released 6 Nov 2006.

Method: X-ray diffraction
Resolution: 1.3 Å
Organisms: HOMO SAPIENS, HIRUDO MEDICINALIS
Chains: 3
Atoms: 2,789
Mol. weight: 34.8 kDa
Ligands: CA, F25
Released: 6 Nov 2006

Explore 2CN0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2CN0 contains 16 α-helices and 24 β-strands across 3 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 H: 13 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-36	7	3
β-strand	38-46	9	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	60-60A	2	4
α-helix	60B-60D	3
β-strand	60F-60G	2	4
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-90	10	3
β-strand	95	1	6
β-strand	100	1	6
β-strand	104-108	5	3
α-helix	111-114	4
β-strand	115	1	7
β-strand	118	1	7
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	165-169	5
α-helix	175-176	2
β-strand	180-183	4	2
α-helix	186-186B	3
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-244	10

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Chain L: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14I	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin precursor	H	protein	257	HOMO SAPIENS	P00734 (AlphaFold model)
Hirudin iia	I	protein	11	HIRUDO MEDICINALIS	P09945 (AlphaFold model)
Prothrombin precursor	L	protein	28	HOMO SAPIENS	P00734 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>2CN0_1 PROTHROMBIN PRECURSOR (chains H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQF

Sequence of entity 2 (I), FASTA

>2CN0_2 HIRUDIN IIA (chains I)
XFEEIPEEYLQ

Sequence of entity 3 (L), FASTA

>2CN0_3 PROTHROMBIN PRECURSOR (chains L)
ADCGLRPLFEKKSLEDKTERELLESYID

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
F25	4-(1R,3AS,4R,8AS,8BR)-[1-difluoromethyl-2-(4-fluorobenzyl)-3-oxodecahydropyrrol…	C24 H27 F3 N4 O	1

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

Primary citation

Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups Into the P Pocket. Hoffmann-Roder, A., Schweizer, E., Egger, J. et al. ChemMedChem (2006) 1:1205. DOI 10.1002/CMDC.200600124 · PubMed

Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFY 1.12 Å, Thrombin in complex with 3-chloro-benzamide
4UD9 1.12 Å, Thrombin in complex with 5-chlorothiophene-2-carboxamide
4UE7 1.13 Å, Thrombin in complex with 1-amidinopiperidine
4UDW 1.16 Å, Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2,…
4UEH 1.16 Å, Thrombin in complex with benzamidine
5AF9 1.18 Å, Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
3RM2 1.23 Å, Human Thrombin in complex with MI003
5AHG 1.24 Å, Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
2BVR 1.25 Å, Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
3VXE 1.25 Å, Human alpha-thrombin-Bivalirudin complex at PD5.0
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104

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