Bromine in PDB 1d3d: Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4

Enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4

All present enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4, PDB code: 1d3d was solved by N.Y.Chirgadze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 2.04
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	71.110, 71.888, 73.321, 90.00, 100.60, 90.00
*R / R_free (%)*	17.5 / 22.3

Other elements in 1d3d:

The structure of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4 (pdb code 1d3d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4, PDB code: 1d3d:

Bromine binding site 1 out of 1 in 1d3d

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Bromine Binding Sites List in 1d3d

Bromine binding site 1 out of 1 in the Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4

Mono view

Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Br400 b:24.4 occ:1.00	BR1	B:BZT400	0.0	24.4	1.0
	C32	B:BZT400	1.8	18.9	1.0
	C15	B:BZT400	2.7	22.0	1.0
	C19	B:BZT400	2.9	24.2	1.0
	C31	B:BZT400	3.4	25.7	1.0
	CZ	B:TYR83	3.5	24.1	1.0
	CE1	B:TYR83	3.6	21.5	1.0
	CE2	B:TYR83	3.7	23.4	1.0
	CD1	B:TYR83	3.8	19.8	1.0
	CD1	B:LEU132	3.8	24.5	1.0
	CD2	B:TYR83	3.8	21.8	1.0
	CG	B:TYR83	3.9	19.3	1.0
	C26	B:BZT400	4.0	35.4	1.0
	CB	B:HIS79	4.0	14.9	1.0
	C13	B:BZT400	4.1	18.7	1.0
	OH	B:TYR83	4.1	26.3	1.0
	C21	B:BZT400	4.1	17.6	1.0
	CZ3	B:TRP86	4.2	30.7	1.0
	CH2	B:TRP86	4.2	30.1	1.0
	CG	B:HIS79	4.2	15.6	1.0
	N2	B:BZT400	4.2	32.9	1.0
	CD2	B:HIS79	4.3	14.6	1.0
	CD2	B:LEU132	4.4	21.8	1.0
	CG	B:LEU132	4.4	23.3	1.0
	C11	B:BZT400	4.6	21.3	1.0
	CE3	B:TRP86	4.7	31.3	1.0
	CZ2	B:TRP86	4.7	32.2	1.0
	CB	B:TYR83	4.8	18.8	1.0

Reference:

N.Y.Chirgadze, D.J.Sall, S.L.Briggs, D.K.Clawson, M.Zhang, G.F.Smith, R.W.Schevitz. The Crystal Structures of Human Alpha-Thrombin Complexed with Active Site-Directed Diamino Benzo[B]Thiophene Derivatives: A Binding Mode For A Structurally Novel Class of Inhibitors Protein Sci. V. 9 29 2000.
ISSN: ISSN 0961-8368
PubMed: 10739244

Page generated: Mon Jul 7 03:03:38 2025

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