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Bromine in PDB 5v9p: Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A

Protein crystallography data

The structure of Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A, PDB code: 5v9p was solved by J.R.Kiefer, J.Liang, M.Vinogradova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.16 / 3.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.949, 158.949, 90.594, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 24.8

Other elements in 5v9p:

The structure of Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Zinc (Zn) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A (pdb code 5v9p). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A, PDB code: 5v9p:

Bromine binding site 1 out of 1 in 5v9p

Go back to Bromine Binding Sites List in 5v9p
Bromine binding site 1 out of 1 in the Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Pyrrolidine Amide Inhibitor [(3S)-3-(4-Bromo-1H- Pyrazol-1-Yl)Pyrrolidin-1-Yl][3-(Propan-2-Yl)-1H-Pyrazol-5- Yl]Methanone (Compound 35) in Complex with KDM5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br904

b:0.0
occ:1.00
BR2 A:90S904 0.0 0.0 1.0
C19 A:90S904 1.9 49.3 1.0
C20 A:90S904 2.9 38.2 1.0
C18 A:90S904 2.9 71.7 1.0
HB3 A:PHE480 3.1 26.2 1.0
HB2 A:ALA411 3.5 27.6 1.0
HD1 A:TYR472 3.6 19.2 1.0
HE1 A:TYR472 3.7 18.8 1.0
HB1 A:ALA411 3.9 27.6 1.0
CB A:PHE480 3.9 21.9 1.0
N21 A:90S904 4.0 31.5 1.0
HB2 A:PHE480 4.0 26.2 1.0
CB A:ALA411 4.1 23.0 1.0
N17 A:90S904 4.1 43.9 1.0
HB3 A:ALA411 4.1 27.6 1.0
HE2 A:TYR409 4.1 43.5 1.0
CD1 A:TYR472 4.2 16.0 1.0
HA A:PHE480 4.2 22.2 1.0
CE1 A:TYR472 4.3 15.7 1.0
O A:HOH1010 4.3 20.5 1.0
O A:SER479 4.4 47.7 1.0
CE2 A:TYR409 4.4 36.3 1.0
O A:HOH1006 4.4 20.5 1.0
CA A:PHE480 4.6 18.5 1.0
HD2 A:TYR409 4.6 37.8 1.0
O1 A:SO4905 4.7 0.4 1.0
CD2 A:TYR409 4.7 31.5 1.0
CG A:PHE480 5.0 17.7 1.0

Reference:

J.Liang, S.Labadie, B.Zhang, D.F.Ortwine, S.Patel, M.Vinogradova, J.R.Kiefer, T.Mauer, V.S.Gehling, J.C.Harmange, R.Cummings, T.Lai, J.Liao, X.Zheng, Y.Liu, A.Gustafson, E.Van Der Porten, W.Mao, B.M.Liederer, G.Deshmukh, L.An, Y.Ran, M.Classon, P.Trojer, P.S.Dragovich, L.Murray. From A Novel Hts Hit to Potent, Selective, and Orally Bioavailable KDM5 Inhibitors. Bioorg. Med. Chem. Lett. V. 27 2974 2017.
ISSN: ESSN 1464-3405
PubMed: 28512031
DOI: 10.1016/J.BMCL.2017.05.016
Page generated: Sat Dec 12 02:31:19 2020

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