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Iodine in PDB 4oc5: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

All present enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc5 was solved by J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.Pomper, J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.578, 130.446, 159.066, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.4

Other elements in 4oc5:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom
Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine (pdb code 4oc5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc5:

Iodine binding site 1 out of 1 in 4oc5

Go back to Iodine Binding Sites List in 4oc5
Iodine binding site 1 out of 1 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Chibzl, A Urea-Based Inhibitor N~2~-{[(S)-Carboxy(4- Hydroxyphenyl)Methyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I818

b:37.9
occ:1.00
IAH A:2QM818 0.0 37.9 1.0
CBC A:2QM818 2.2 35.8 1.0
CAL A:2QM818 3.2 36.9 1.0
CAK A:2QM818 3.2 37.6 1.0
O A:ARG463 3.7 26.6 1.0
CG A:ARG534 3.8 25.2 1.0
CG A:ARG463 3.8 24.9 1.0
C A:ARG463 3.9 25.6 1.0
CG A:ARG536 4.1 25.2 1.0
CD A:ARG463 4.1 28.5 1.0
N A:ASP465 4.1 23.1 1.0
CB A:ARG463 4.2 24.5 1.0
N A:VAL464 4.2 23.8 1.0
CA A:VAL464 4.2 23.2 1.0
O A:ARG534 4.2 21.9 1.0
CD A:ARG534 4.2 25.7 1.0
NE A:ARG534 4.3 27.3 1.0
N A:ARG536 4.3 22.8 1.0
CA A:ALA535 4.3 22.4 1.0
C A:VAL464 4.3 24.0 1.0
C A:ARG534 4.4 22.1 1.0
CG A:ASP465 4.4 32.8 1.0
OD1 A:ASP465 4.4 36.2 1.0
N A:ALA535 4.4 23.0 1.0
NE A:ARG463 4.5 29.1 1.0
C A:ALA535 4.5 24.1 1.0
CAN A:2QM818 4.5 37.5 1.0
CAM A:2QM818 4.6 37.4 1.0
NE A:ARG536 4.6 33.2 1.0
CD A:ARG536 4.6 28.7 1.0
CB A:ASP465 4.6 24.1 1.0
CB A:ARG534 4.6 22.4 1.0
CA A:ARG463 4.7 24.6 1.0
OD2 A:ASP465 4.7 36.0 1.0
CZ A:ARG534 4.8 26.8 1.0
O A:HOH1393 4.9 36.3 1.0
CB A:ARG536 4.9 24.2 1.0

Reference:

J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.G.Pomper, J.Lubkowski, C.Barinka. Structural Characterization of P1'-Diversified Urea-Based Inhibitors of Glutamate Carboxypeptidase II. Bioorg.Med.Chem.Lett. V. 24 2340 2014.
ISSN: ISSN 0960-894X
PubMed: 24731280
DOI: 10.1016/J.BMCL.2014.03.066
Page generated: Sun Dec 13 19:35:37 2020

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