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Zinc in PDB 5h4j: Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide

Enzymatic activity of Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide

All present enzymatic activity of Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide:
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide, PDB code: 5h4j was solved by K.T.Chong, S.Miyahara, H.Miyakoshi, M.Fukuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.76 / 1.80
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 89.645, 89.645, 89.645, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 17.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide (pdb code 5h4j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide, PDB code: 5h4j:

Zinc binding site 1 out of 1 in 5h4j

Go back to Zinc Binding Sites List in 5h4j
Zinc binding site 1 out of 1 in the Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Dutpase in Complex with N-[(1R)-1-[3- (Cyclopentyloxy)-Phenyl]-Ethyl]-3-[(3,4-Dihydro-2,4-Dioxo-1(2H)- Pyrimidinyl)Methoxy]-1-Propanesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:19.6
occ:1.00
 N1 A:IMD203 2.0 18.5 1.0
NE2 A:HIS34 2.1 19.8 1.0
C5 A:IMD203 3.0 20.9 1.0
CD2 A:HIS34 3.1 18.1 1.0
CE1 A:HIS34 3.1 19.5 1.0
C2 A:IMD203 3.1 18.5 1.0
C4 A:IMD203 4.2 20.7 1.0
N3 A:IMD203 4.2 20.0 1.0
ND1 A:HIS34 4.2 18.0 1.0
CG A:HIS34 4.2 17.8 1.0
OE1 A:GLU33 4.3 19.4 1.0
CE1 A:TYR54 4.6 17.3 1.0
O A:HOH440 4.8 34.6 0.3
CD A:GLU33 4.9 18.6 1.0
OH A:TYR54 4.9 18.5 1.0

Reference:

W.Yano, T.Yokogawa, T.Wakasa, K.Yamamura, A.Fujioka, K.Yoshisue, E.Matsushima, S.Miyahara, H.Miyakoshi, J.Taguchi, K.T.Chong, Y.Takao, M.Fukuoka, K.Matsuo. Tas-114, A First-in-Class Dual Dutpase/Dpd Inhibitor, Demonstrates Potential to Improve Therapeutic Efficacy of Fluoropyrimidine-Based Chemotherapy. Mol. Cancer Ther. V. 17 1683 2018.
ISSN: ESSN 1538-8514
PubMed: 29748212
DOI: 10.1158/1535-7163.MCT-17-0911
Page generated: Sun Oct 27 17:20:11 2024

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