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Chlorine in PDB 5vd3: Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib

Enzymatic activity of Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib

All present enzymatic activity of Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib, PDB code: 5vd3 was solved by J.-Y.Zhu, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.11 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.040, 54.060, 114.110, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib (pdb code 5vd3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib, PDB code: 5vd3:

Chlorine binding site 1 out of 1 in 5vd3

Go back to Chlorine Binding Sites List in 5vd3
Chlorine binding site 1 out of 1 in the Crystal Structure of Human MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib


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 MYT1 Kinase Domain (De-Phosphorylated) in Complex with Saracatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:19.7
occ:1.00
 CL3 A:H8H401 0.0 19.7 1.0
C30 A:H8H401 1.7 16.6 1.0
C29 A:H8H401 2.7 16.6 1.0
C22 A:H8H401 2.7 15.9 1.0
HZ A:PHE240 2.8 21.2 1.0
H29 A:H8H401 2.8 20.0 1.0
HN21 A:H8H401 2.8 19.2 1.0
N21 A:H8H401 3.0 16.0 1.0
H22 A:EDO403 3.2 69.1 1.0
HB2 A:ASP251 3.3 21.9 1.0
O A:HOH634 3.6 31.5 1.0
CZ A:PHE240 3.7 17.8 1.0
H182 A:H8H401 3.7 35.2 1.0
C28 A:H8H401 4.0 17.3 1.0
H141 A:H8H401 4.0 34.2 1.0
C23 A:H8H401 4.0 16.0 1.0
O16 A:H8H401 4.0 36.8 1.0
HB3 A:ASN238 4.0 24.2 1.0
HE2 A:PHE240 4.0 22.0 1.0
C20 A:H8H401 4.1 15.2 1.0
CG A:ASP251 4.1 29.1 1.0
CB A:ASP251 4.1 18.2 1.0
O12 A:H8H401 4.2 19.5 1.0
HO2 A:EDO403 4.2 69.9 1.0
C2 A:EDO403 4.2 57.6 1.0
OD1 A:ASP251 4.2 24.5 1.0
HA A:ASN238 4.3 20.9 1.0
CE2 A:PHE240 4.3 18.3 1.0
O2 A:EDO403 4.4 58.2 1.0
HA A:ASP251 4.5 20.7 1.0
C27 A:H8H401 4.5 16.0 1.0
C18 A:H8H401 4.5 29.4 1.0
HG21 A:VAL124 4.5 18.8 1.0
OD2 A:ASP251 4.5 22.4 1.0
O A:ALA237 4.5 17.7 1.0
H11 A:EDO403 4.6 67.0 1.0
H171 A:H8H401 4.6 42.9 1.0
HB2 A:ASN238 4.6 24.2 1.0
C17 A:H8H401 4.6 35.7 1.0
C14 A:H8H401 4.7 28.5 1.0
CB A:ASN238 4.7 20.1 1.0
H151 A:H8H401 4.7 41.2 1.0
C15 A:H8H401 4.7 34.3 1.0
CE1 A:PHE240 4.7 19.6 1.0
HE1 A:PHE240 4.7 23.5 1.0
N32 A:H8H401 4.8 17.5 1.0
C13 A:H8H401 4.8 24.7 1.0
CA A:ASP251 4.8 17.3 1.0
H28 A:H8H401 4.8 20.8 1.0
HB3 A:ASP251 4.9 21.9 1.0
H21 A:EDO403 4.9 69.1 1.0
C19 A:H8H401 5.0 14.3 1.0
H A:ASP251 5.0 20.7 1.0

Reference:

J.Y.Zhu, R.A.Cuellar, N.Berndt, H.E.Lee, S.H.Olesen, M.P.Martin, J.T.Jensen, G.I.Georg, E.Schonbrunn. Structural Basis of Wee Kinases Functionality and Inactivation By Diverse Small Molecule Inhibitors. J. Med. Chem. V. 60 7863 2017.
ISSN: ISSN 1520-4804
PubMed: 28792760
DOI: 10.1021/ACS.JMEDCHEM.7B00996
Page generated: Sat Jul 12 09:51:10 2025

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