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Chlorine in PDB 2p3t: Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide

Enzymatic activity of Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide

All present enzymatic activity of Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide, PDB code: 2p3t 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) 19.88 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.060, 72.510, 78.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.1

Other elements in 2p3t:

The structure of Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide (pdb code 2p3t). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide, PDB code: 2p3t:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2p3t

Go back to Chlorine Binding Sites List in 2p3t
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide


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 Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:34.7
occ:1.00
 N B:THR113 3.0 22.2 1.0
NE2 B:HIS83 3.0 26.9 1.0
NH1 B:ARG115 3.2 38.9 1.0
O B:HOH630 3.2 42.4 1.0
CB B:ALA81 3.4 30.2 1.0
NH2 B:ARG115 3.5 40.8 1.0
CA B:ILE112 3.7 20.9 1.0
CE1 B:HIS83 3.8 28.9 1.0
CB B:THR113 3.8 24.9 1.0
CZ B:ARG115 3.8 41.9 1.0
C B:ILE112 3.8 20.1 1.0
CA B:THR113 3.9 21.9 1.0
CG2 B:ILE112 4.0 17.6 1.0
O B:THR113 4.0 16.6 1.0
CD2 B:HIS83 4.1 26.0 1.0
OG1 B:THR113 4.1 29.1 1.0
CG2 B:VAL68 4.4 16.2 1.0
CB B:ILE112 4.4 21.4 1.0
C B:THR113 4.4 17.9 1.0
O B:PRO111 4.5 20.2 1.0
N B:ILE112 4.9 19.3 1.0
CG1 B:ILE112 4.9 20.2 1.0
CA B:ALA81 4.9 32.1 1.0

Chlorine binding site 2 out of 4 in 2p3t

Go back to Chlorine Binding Sites List in 2p3t
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide


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 Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl500

b:31.1
occ:1.00
 CL3 B:993500 0.0 31.1 1.0
C26 B:993500 1.7 31.1 1.0
C25 B:993500 2.8 30.1 1.0
C22 B:993500 2.8 31.5 1.0
N19 B:993500 3.0 29.8 1.0
C28 B:993500 3.2 30.4 1.0
O B:HOH631 3.3 31.3 1.0
C20 B:993500 3.4 33.0 1.0
O B:HOH568 3.5 30.8 1.0
O10 B:993500 3.7 23.8 1.0
CB B:TRP215 3.9 20.5 1.0
OH B:TYR99 3.9 34.8 1.0
O B:HOH615 4.0 42.3 1.0
C24 B:993500 4.0 31.6 1.0
CE2 B:TYR99 4.0 32.5 1.0
CZ B:TYR99 4.0 34.7 1.0
C12 B:993500 4.2 32.6 1.0
S23 B:993500 4.2 32.4 1.0
O B:HOH617 4.3 53.2 1.0
O21 B:993500 4.6 27.3 1.0
C9 B:993500 4.7 23.9 1.0
N29 B:993500 4.7 34.3 1.0
CD2 B:TYR99 4.7 31.8 1.0
CE1 B:TYR99 4.8 33.1 1.0
CA B:TRP215 4.8 20.6 1.0
O B:GLY216 4.8 20.6 1.0
CG B:TRP215 4.9 17.8 1.0
C11 B:993500 4.9 29.6 1.0
C18 B:993500 4.9 42.1 1.0
N B:GLY216 5.0 22.3 1.0

Chlorine binding site 3 out of 4 in 2p3t

Go back to Chlorine Binding Sites List in 2p3t
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide


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 Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl500

b:31.7
occ:1.00
 CL2 B:993500 0.0 31.7 1.0
C15 B:993500 1.7 34.4 1.0
C16 B:993500 2.7 30.6 1.0
C14 B:993500 2.7 35.5 1.0
O B:GLU146 3.3 29.2 1.0
NH1 B:ARG143 3.7 37.0 1.0
CG B:GLU146 3.7 27.8 1.0
SG B:CYS220 3.8 30.9 1.0
CB B:GLN192 3.8 31.8 1.0
CG B:GLN192 4.0 39.8 1.0
C11 B:993500 4.0 29.6 1.0
C13 B:993500 4.0 35.1 1.0
SG B:CYS191 4.1 27.2 1.0
C B:GLU146 4.2 29.4 1.0
CA B:GLU146 4.2 27.8 1.0
CD B:ARG143 4.4 32.0 1.0
CZ B:ARG143 4.5 37.6 1.0
CB B:GLU146 4.6 26.7 1.0
C12 B:993500 4.6 32.6 1.0
N B:GLN192 4.6 24.7 1.0
NE B:ARG143 4.7 35.3 1.0
CD B:GLU146 4.8 30.6 1.0
CA B:GLN192 4.8 26.2 1.0
C B:GLY218 4.9 29.0 1.0
CA B:GLY218 4.9 28.8 1.0

Chlorine binding site 4 out of 4 in 2p3t

Go back to Chlorine Binding Sites List in 2p3t
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Factor Xa Complexed with 3- Chloro-4-(2-Methylamino-Imidazol-1-Ylmethyl)-Thiophene-2- Carboxylic Acid [4-Chloro-2-(5-Chloro-Pyridin-2- Ylcarbamoyl)-6-Methoxy-Phenyl]-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl500

b:19.3
occ:1.00
 CL1 B:993500 0.0 19.3 1.0
C4 B:993500 1.7 20.6 1.0
C5 B:993500 2.7 19.4 1.0
C3 B:993500 2.7 18.3 1.0
N B:ILE227 3.5 16.5 1.0
CZ B:TYR228 3.6 18.2 1.0
CA B:GLY226 3.6 19.1 1.0
O B:ILE227 3.6 15.3 1.0
CG1 B:VAL213 3.6 12.2 1.0
O B:TRP215 3.7 19.9 1.0
CB B:ALA190 3.7 17.9 1.0
CE1 B:TYR228 3.7 19.4 1.0
OH B:TYR228 3.8 19.0 1.0
C B:GLY226 3.8 17.6 1.0
CE2 B:TYR228 4.0 16.8 1.0
N2 B:993500 4.0 19.1 1.0
C6 B:993500 4.0 19.1 1.0
C B:ILE227 4.2 16.3 1.0
CD1 B:TYR228 4.3 19.4 1.0
N B:SER214 4.4 18.8 1.0
C B:TRP215 4.4 20.0 1.0
CA B:ILE227 4.5 18.0 1.0
OD1 B:ASP189 4.5 20.0 1.0
CD2 B:TYR228 4.5 19.7 1.0
N B:TRP215 4.5 19.9 1.0
C1 B:993500 4.5 21.0 1.0
O B:HOH588 4.6 22.6 1.0
CG B:TYR228 4.6 20.7 1.0
CA B:VAL213 4.6 16.6 1.0
CB B:VAL213 4.7 15.5 1.0
O B:GLY226 4.8 18.3 1.0
CA B:ALA190 4.8 20.7 1.0
CA B:TRP215 4.9 20.6 1.0
C B:VAL213 4.9 18.2 1.0
N B:ALA190 5.0 22.0 1.0
N B:GLY226 5.0 22.4 1.0

Reference:

B.Ye, D.O.Arnaiz, Y.L.Chou, B.D.Griedel, R.Karanjawala, W.Lee, M.M.Morrissey, K.L.Sacchi, S.T.Sakata, K.J.Shaw, S.C.Wu, Z.Zhao, M.Adler, S.Cheeseman, W.P.Dole, J.Ewing, R.Fitch, D.Lentz, A.Liang, D.Light, J.Morser, J.Post, G.Rumennik, B.Subramanyam, M.E.Sullivan, R.Vergona, J.Walters, Y.X.Wang, K.A.White, M.Whitlow, M.J.Kochanny. Thiophene-Anthranilamides As Highly Potent and Orally Available Factor Xa Inhibitors. J.Med.Chem. V. 50 2967 2007.
ISSN: ISSN 0022-2623
PubMed: 17536795
DOI: 10.1021/JM070125F
Page generated: Thu Jul 10 23:45:25 2025

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