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Calcium 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:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was 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:

Calcium binding site 1 out of 1 in 2p3t

Go back to Calcium Binding Sites List in 2p3t
Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca501

b:46.5
occ:1.00
 OD2 B:ASP70 2.3 41.3 1.0
OE1 B:GLU80 2.3 49.7 1.0
O B:ASN72 2.4 30.8 1.0
O B:GLU76 2.6 69.2 1.0
O B:GLN75 2.6 63.0 1.0
C B:GLU76 3.2 67.7 1.0
O B:HOH590 3.2 35.7 1.0
CD B:GLU80 3.3 48.0 1.0
C B:ASN72 3.4 32.4 1.0
CG B:ASP70 3.5 38.9 1.0
C B:GLN75 3.6 62.7 1.0
CG B:GLU80 3.7 43.7 1.0
OD1 B:ASP70 4.0 42.3 1.0
N B:ASN72 4.2 29.1 1.0
CA B:GLU76 4.3 66.4 1.0
N B:GLU76 4.3 64.8 1.0
N B:THR73 4.3 34.7 1.0
CA B:ASN72 4.3 31.0 1.0
CG B:GLU76 4.3 66.3 1.0
CA B:THR73 4.4 39.7 1.0
N B:GLN75 4.4 57.1 1.0
OE2 B:GLU80 4.4 50.2 1.0
CA B:GLN75 4.5 60.8 1.0
C B:THR73 4.6 42.3 1.0
CB B:ASP70 4.6 32.3 1.0
CB B:ASN72 4.7 33.5 1.0
CA B:ASP70 4.7 28.5 1.0
N B:ARG71 4.8 21.8 1.0
OE2 B:GLU76 4.8 68.0 1.0
N B:GLU74 4.8 46.0 1.0
CB B:GLU76 4.9 65.8 1.0
O B:THR73 5.0 44.1 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: Tue Jul 8 07:35:43 2025

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