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Chlorine in PDB 1mq6: Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa

Enzymatic activity of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa

All present enzymatic activity of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa, PDB code: 1mq6 was solved by M.Adler, M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.640, 73.290, 79.020, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 26.8

Other elements in 1mq6:

The structure of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa (pdb code 1mq6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa, PDB code: 1mq6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 1mq6

Go back to Chlorine Binding Sites List in 1mq6
Chlorine binding site 1 out of 3 in the Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl500

b:27.7
occ:1.00
 CL1 A:XLD500 0.0 27.7 1.0
C4 A:XLD500 1.8 29.2 1.0
C3 A:XLD500 2.8 28.4 1.0
C5 A:XLD500 2.8 25.4 1.0
CZ A:TYR228 3.4 19.5 1.0
OH A:TYR228 3.4 18.2 1.0
CA A:GLY226 3.6 22.8 1.0
CE1 A:TYR228 3.6 20.3 1.0
CB A:ALA190 3.7 21.3 1.0
N A:ILE227 3.7 23.1 1.0
CG1 A:VAL213 3.7 16.6 1.0
O A:ILE227 3.8 28.6 1.0
C A:GLY226 3.9 24.4 1.0
O A:TRP215 3.9 30.9 1.0
CE2 A:TYR228 3.9 19.3 1.0
N2 A:XLD500 4.0 31.0 1.0
C6 A:XLD500 4.1 28.7 1.0
CD1 A:TYR228 4.3 18.7 1.0
O A:HOH662 4.4 16.2 1.0
C A:ILE227 4.4 24.5 1.0
OD1 A:ASP189 4.5 34.8 1.0
CD2 A:TYR228 4.5 18.8 1.0
N A:SER214 4.5 24.9 1.0
C1 A:XLD500 4.6 32.4 1.0
C A:TRP215 4.7 28.5 1.0
N A:TRP215 4.7 29.8 1.0
CG A:TYR228 4.7 19.1 1.0
CA A:VAL213 4.7 24.1 1.0
CA A:ILE227 4.7 25.0 1.0
CB A:VAL213 4.7 25.2 1.0
O A:GLY226 4.8 23.8 1.0
CA A:ALA190 4.8 27.7 1.0
N A:ALA190 4.9 30.4 1.0
N A:GLY226 4.9 25.1 1.0

Chlorine binding site 2 out of 3 in 1mq6

Go back to Chlorine Binding Sites List in 1mq6
Chlorine binding site 2 out of 3 in the Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl500

b:37.5
occ:1.00
 CL2 A:XLD500 0.0 37.5 1.0
C15 A:XLD500 1.7 38.1 1.0
C16 A:XLD500 2.6 37.4 1.0
C14 A:XLD500 2.7 38.0 1.0
O A:GLU146 3.4 31.4 1.0
CG A:GLU146 3.7 32.4 1.0
SG A:CYS220 3.7 37.4 1.0
SG A:CYS191 4.0 32.5 1.0
C11 A:XLD500 4.0 38.3 1.0
NH1 A:ARG143 4.0 42.6 1.0
C13 A:XLD500 4.0 37.8 1.0
CB A:GLN192 4.0 40.3 1.0
CA A:GLU146 4.2 33.8 1.0
C A:GLU146 4.2 34.5 1.0
CD A:ARG143 4.3 31.1 1.0
O A:HOH740 4.3 78.5 1.0
CZ A:ARG143 4.3 41.2 1.0
O A:HOH696 4.3 57.0 1.0
NE A:ARG143 4.4 36.0 1.0
NE2 A:GLN192 4.5 67.9 1.0
CD A:GLN192 4.5 61.9 1.0
C12 A:XLD500 4.5 37.9 1.0
CB A:GLU146 4.5 34.2 1.0
N A:GLN192 4.6 31.0 1.0
CG A:GLN192 4.8 49.3 1.0
OE1 A:GLN192 4.8 67.3 1.0
CD A:GLU146 4.8 35.3 1.0
C A:GLY218 4.9 33.1 1.0
CA A:GLN192 5.0 32.3 1.0
NH2 A:ARG143 5.0 43.2 1.0
CA A:GLY218 5.0 30.4 1.0

Chlorine binding site 3 out of 3 in 1mq6

Go back to Chlorine Binding Sites List in 1mq6
Chlorine binding site 3 out of 3 in the Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of 3-Chloro-N-[4-Chloro-2-[[(5-Chloro-2-Pyridinyl) Amino]Carbonyl]-6-Methoxyphenyl]-4-[[(4,5-Dihydro-2-Oxazolyl) Methylamino]Methyl]-2-Thiophenecarboxamide Complexed with Human Factor Xa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl500

b:37.3
occ:1.00
 CL3 A:XLD500 0.0 37.3 1.0
C26 A:XLD500 1.7 37.3 1.0
C25 A:XLD500 2.7 39.2 1.0
C22 A:XLD500 2.8 38.5 1.0
C28 A:XLD500 3.1 40.2 1.0
N19 A:XLD500 3.2 36.4 1.0
C20 A:XLD500 3.4 35.8 1.0
CB A:TRP215 3.6 27.0 1.0
CE2 A:TYR99 3.6 35.9 1.0
OH A:TYR99 3.7 48.1 1.0
CZ A:TYR99 3.8 41.0 1.0
O10 A:XLD500 3.9 39.0 1.0
O A:HOH724 3.9 72.5 1.0
C24 A:XLD500 3.9 38.3 1.0
S23 A:XLD500 4.3 40.5 1.0
C12 A:XLD500 4.4 37.9 1.0
CD2 A:TYR99 4.4 37.2 1.0
CA A:TRP215 4.6 28.5 1.0
CG A:TRP215 4.6 26.2 1.0
O21 A:XLD500 4.6 30.6 1.0
N29 A:XLD500 4.7 43.1 1.0
CE1 A:TYR99 4.7 39.2 1.0
C9 A:XLD500 4.8 38.4 1.0
O A:GLY216 4.8 33.1 1.0
N A:GLY216 4.9 30.9 1.0

Reference:

M.Adler, M.J.Kochanny, Y.Bin, G.Rumennik, D.L.Light, S.Biancalana, M.Whitlow. Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa Biochemistry V. 41 15514 2002.
ISSN: ISSN 0006-2960
PubMed: 12501180
DOI: 10.1021/BI0264061
Page generated: Sat Jul 20 00:11:35 2024

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