1NM6: Thrombin

thrombin in complex with selective macrocyclic inhibitor at 1.8A. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Sept 2003.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,562
Mol. weight: 35.02 kDa
Ligands: L86
Released: 2 Sept 2003

Explore 1NM6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NM6 contains 17 α-helices and 22 β-strands across 2 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: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14I	7
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	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
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	165-170	6
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 B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	356-360	5
α-helix	361-364	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
thrombin	A	protein	287	Homo sapiens	P00734 (AlphaFold model)
Hirudin	B	protein	11		P28504 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1NM6_1 thrombin (chains A)
DCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGAS
LISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYN
WRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTAN
VGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVM
KSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG

Sequence of entity 2 (B), FASTA

>1NM6_2 Hirudin (chains B)
DFEEIPEEYLA

Ligands and cofactors

ID	Name	Formula	Copies
L86	(11S)-11-benzyl-6-chloro-1,2,10,11,12,13,14,15,16,17,18,19-dodecahydro-5,9-meth…	C27 H33 Cl N6 O2	1

Primary citation

Design and synthesis of potent and selective macrocyclic thrombin inhibitors. Nantermet, P.G., Barrow, J.C., Newton, C.L. et al. Bioorg Med Chem Lett (2003) 13:2781-2784. DOI 10.1016/S0960-894X(03)00506-7 · 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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