Nickel in PDB 5v9t: Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48)

The structure of Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48), PDB code: 5v9t 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)	34.54 / 3.05
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	159.615, 159.615, 92.071, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 29

The structure of Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48) (pdb code 5v9t). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48), PDB code: 5v9t:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:59.0 occ:1.00 H8 A:90V904 1.4 83.2 1.0 N7 A:90V904 1.9 69.4 1.0 O11 A:90V904 1.9 0.6 1.0 NE2 A:HIS483 1.9 0.3 1.0 NE2 A:HIS571 2.0 93.8 1.0 C6 A:90V904 2.3 98.1 1.0 HE1 A:HIS483 2.3 0.9 1.0 C10 A:90V904 2.4 93.5 1.0 CE1 A:HIS483 2.4 0.2 1.0 HE1 A:HIS571 2.4 0.4 1.0 OE2 A:GLU485 2.4 41.6 1.0 CE1 A:HIS571 2.5 86.3 1.0 CD2 A:HIS483 3.1 42.0 1.0 N9 A:90V904 3.2 79.2 1.0 CD2 A:HIS571 3.3 88.7 1.0 ND1 A:HIS483 3.6 41.8 1.0 C5 A:90V904 3.6 59.0 1.0 HD2 A:HIS483 3.6 50.2 1.0 CD A:GLU485 3.6 41.8 1.0 ND1 A:HIS571 3.8 48.5 1.0 HD2 A:HIS571 3.8 0.2 1.0 N12 A:90V904 3.8 59.0 1.0 C4 A:90V904 4.0 59.0 1.0 CG A:HIS483 4.0 42.2 1.0 HB2 A:SER491 4.2 59.1 1.0 CG A:HIS571 4.2 42.9 1.0 OG A:SER491 4.3 64.8 1.0 HD1 A:HIS483 4.3 50.0 1.0 OE1 A:GLU485 4.3 0.1 1.0 HD21 A:ASN493 4.3 0.6 1.0 H51 A:90V904 4.3 70.7 1.0 HB3 A:SER491 4.4 59.1 1.0 HD1 A:HIS571 4.5 58.0 1.0 CB A:SER491 4.5 49.4 1.0 HG2 A:GLU485 4.5 50.7 1.0 H172 A:90V904 4.6 77.4 1.0 HZ3 A:TRP503 4.6 54.3 1.0 C17 A:90V904 4.6 64.7 1.0 HG21 A:THR565 4.7 91.4 1.0 CG A:GLU485 4.7 42.4 1.0 H171 A:90V904 4.7 77.4 1.0 HG A:SER491 4.8 77.6 1.0 HH2 A:TRP503 4.9 53.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Selective Pyrrolidine Amide KDM5A Inhibitor N- {(3R)-1-[3-(Propan-2-Yl)-1H-Pyrazole-5-Carbonyl]Pyrrolidin-3- Yl}Cyclopropanecarboxamide (Compound 48) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni901 b:59.0 occ:1.00 H8 B:90V904 1.5 70.7 1.0 N7 B:90V904 1.9 59.0 1.0 NE2 B:HIS483 2.0 87.3 1.0 O11 B:90V904 2.0 0.2 1.0 NE2 B:HIS571 2.1 70.6 1.0 OE2 B:GLU485 2.2 81.1 1.0 C6 B:90V904 2.3 60.5 1.0 C10 B:90V904 2.4 82.0 1.0 CE1 B:HIS483 2.6 79.9 1.0 HE1 B:HIS483 2.6 95.7 1.0 HE1 B:HIS571 2.8 72.5 1.0 CE1 B:HIS571 2.8 60.5 1.0 N9 B:90V904 3.1 84.5 1.0 CD2 B:HIS483 3.2 0.9 1.0 CD2 B:HIS571 3.3 50.6 1.0 CD B:GLU485 3.4 75.6 1.0 C5 B:90V904 3.5 59.0 1.0 HD2 B:HIS483 3.6 0.9 1.0 HG B:SER491 3.7 79.7 1.0 HD2 B:HIS571 3.7 60.6 1.0 ND1 B:HIS483 3.8 53.4 1.0 C4 B:90V904 3.8 59.0 1.0 N12 B:90V904 3.9 59.0 1.0 OE1 B:GLU485 4.0 98.0 1.0 ND1 B:HIS571 4.0 39.2 1.0 CG B:HIS483 4.1 39.8 1.0 H51 B:90V904 4.2 70.7 1.0 CG B:HIS571 4.3 38.8 1.0 HB2 B:SER491 4.4 53.2 1.0 OG B:SER491 4.4 66.5 1.0 HG2 B:GLU485 4.4 89.3 1.0 HD21 B:ASN493 4.5 0.3 1.0 HD1 B:HIS483 4.5 63.9 1.0 HB3 B:SER491 4.5 53.2 1.0 HZ3 B:TRP503 4.5 78.9 1.0 CG B:GLU485 4.5 74.5 1.0 HG1 B:THR565 4.7 59.4 1.0 CB B:SER491 4.7 44.5 1.0 H172 B:90V904 4.7 0.3 1.0 HD1 B:HIS571 4.7 46.9 1.0 C17 B:90V904 4.7 89.5 1.0 HG21 B:THR565 4.8 64.8 1.0 O B:HOH1004 4.8 59.0 1.0 H171 B:90V904 4.8 0.3 1.0 HH2 B:TRP503 4.9 60.3 1.0 HG3 B:GLU485 4.9 89.3 1.0

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