Fluorine in PDB 6q13: Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution

All present enzymatic activity of Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution:
1.1.1.27;

The structure of Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution, PDB code: 6q13 was solved by D.R.Davies, D.M.Dranow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.14 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.800, 94.740, 121.560, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.9

The binding sites of Fluorine atom in the Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution (pdb code 6q13). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution, PDB code: 6q13:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:23.7 occ:1.00 F35 A:P8V402 0.0 23.7 1.0 C33 A:P8V402 1.3 23.4 1.0 C34 A:P8V402 2.3 22.6 1.0 C32 A:P8V402 2.4 25.0 1.0 O38 A:P8V402 2.9 22.4 1.0 S36 A:P8V402 3.0 22.8 1.0 N A:VAL139 3.2 20.2 1.0 N37 A:P8V402 3.4 21.3 1.0 CG1 A:VAL139 3.5 19.0 1.0 OD2 A:ASP140 3.6 19.1 1.0 CB A:HIS192 3.6 22.8 1.0 C29 A:P8V402 3.6 25.3 1.0 C31 A:P8V402 3.6 26.9 1.0 O A:HIS192 3.7 21.8 1.0 OD1 A:ASN137 3.7 26.4 1.0 N A:ASP140 3.8 18.1 1.0 C A:PRO138 3.9 23.1 1.0 CD2 A:HIS192 4.0 26.5 1.0 CA A:PRO138 4.0 20.6 1.0 C30 A:P8V402 4.1 24.2 1.0 CG A:HIS192 4.1 22.6 1.0 CA A:VAL139 4.2 16.3 1.0 N A:HIS192 4.2 23.0 1.0 CA A:HIS192 4.3 26.5 1.0 CG A:ASP140 4.3 29.5 1.0 C A:HIS192 4.3 28.7 1.0 CB A:PRO138 4.3 23.6 1.0 CB A:VAL139 4.3 21.3 1.0 O39 A:P8V402 4.5 28.3 1.0 C A:VAL139 4.5 18.5 1.0 CB A:ASP140 4.6 30.3 1.0 O A:PRO138 4.8 20.7 1.0 CA A:ASP140 4.9 19.9 1.0 C28 A:P8V402 4.9 23.5 1.0 CG A:ASN137 4.9 28.1 1.0 O A:HOH511 4.9 27.9 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:24.4 occ:1.00 F35 B:P8V402 0.0 24.4 1.0 C33 B:P8V402 1.4 24.6 1.0 C34 B:P8V402 2.3 22.7 1.0 C32 B:P8V402 2.4 25.1 1.0 O38 B:P8V402 3.0 27.1 1.0 S36 B:P8V402 3.0 25.6 1.0 N37 B:P8V402 3.3 16.9 1.0 N B:VAL139 3.3 25.4 1.0 OD1 B:ASN137 3.5 22.1 1.0 O B:HIS192 3.6 24.1 1.0 CG1 B:VAL139 3.6 23.2 1.0 CB B:HIS192 3.6 24.7 1.0 C29 B:P8V402 3.6 24.5 1.0 C31 B:P8V402 3.6 22.7 1.0 OD2 B:ASP140 3.6 28.0 1.0 CD2 B:HIS192 3.8 29.8 1.0 N B:ASP140 4.0 24.0 1.0 C B:PRO138 4.0 23.6 1.0 CA B:PRO138 4.0 28.3 1.0 CG B:HIS192 4.1 27.2 1.0 C30 B:P8V402 4.1 21.9 1.0 C B:HIS192 4.2 27.6 1.0 CA B:HIS192 4.2 19.3 1.0 N B:HIS192 4.3 18.4 1.0 CA B:VAL139 4.3 21.1 1.0 CB B:PRO138 4.3 30.5 1.0 CG B:ASP140 4.4 26.8 1.0 CB B:VAL139 4.5 24.1 1.0 O39 B:P8V402 4.5 19.8 1.0 C B:VAL139 4.7 22.7 1.0 CG B:ASN137 4.7 28.9 1.0 CB B:ASP140 4.7 26.5 1.0 C28 B:P8V402 4.8 24.9 1.0 O B:PRO138 4.9 26.7 1.0 CA B:ASP140 5.0 22.6 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:28.1 occ:1.00 F35 C:P8V402 0.0 28.1 1.0 C33 C:P8V402 1.4 31.2 1.0 C34 C:P8V402 2.3 30.1 1.0 C32 C:P8V402 2.4 20.7 1.0 O39 C:P8V402 2.8 25.2 1.0 S36 C:P8V402 3.0 27.8 1.0 N C:VAL139 3.3 26.7 1.0 N37 C:P8V402 3.4 25.7 1.0 OD2 C:ASP140 3.5 27.1 1.0 CG1 C:VAL139 3.5 28.4 1.0 OD1 C:ASN137 3.6 32.9 1.0 CB C:HIS192 3.6 28.1 1.0 C29 C:P8V402 3.6 32.7 1.0 C31 C:P8V402 3.6 26.4 1.0 O C:HIS192 3.7 28.1 1.0 N C:ASP140 3.9 27.4 1.0 CD2 C:HIS192 3.9 30.6 1.0 C C:PRO138 3.9 30.4 1.0 CA C:PRO138 4.0 28.9 1.0 C30 C:P8V402 4.1 33.6 1.0 CG C:HIS192 4.1 27.6 1.0 CA C:VAL139 4.3 26.3 1.0 CG C:ASP140 4.3 29.6 1.0 CA C:HIS192 4.3 26.3 1.0 CB C:PRO138 4.3 31.6 1.0 N C:HIS192 4.3 30.3 1.0 C C:HIS192 4.3 28.2 1.0 CB C:VAL139 4.4 29.2 1.0 O38 C:P8V402 4.5 33.9 1.0 C C:VAL139 4.6 27.9 1.0 CB C:ASP140 4.6 31.6 1.0 CG C:ASN137 4.7 30.8 1.0 C28 C:P8V402 4.9 23.2 1.0 O C:PRO138 4.9 30.5 1.0 CA C:ASP140 4.9 30.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Ldha in Complex with Compound NCGC00420737-09 at 2.00 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:F402 b:29.3 occ:1.00 F35 D:P8V402 0.0 29.3 1.0 C33 D:P8V402 1.4 35.3 1.0 C32 D:P8V402 2.3 33.3 1.0 C34 D:P8V402 2.4 29.9 1.0 O38 D:P8V402 2.9 28.5 1.0 S36 D:P8V402 2.9 26.8 1.0 N37 D:P8V402 3.3 21.3 1.0 N D:VAL139 3.3 25.9 1.0 CG1 D:VAL139 3.5 30.9 1.0 OD1 D:ASN137 3.5 35.5 1.0 OD2 D:ASP140 3.6 26.7 1.0 O D:HIS192 3.6 29.6 1.0 C29 D:P8V402 3.6 26.6 1.0 C31 D:P8V402 3.6 28.0 1.0 CB D:HIS192 3.6 24.9 1.0 N D:ASP140 3.8 27.3 1.0 C D:PRO138 3.9 29.0 1.0 CA D:PRO138 4.0 32.0 1.0 CD2 D:HIS192 4.1 30.9 1.0 C30 D:P8V402 4.1 25.3 1.0 CA D:VAL139 4.2 31.2 1.0 CG D:HIS192 4.2 30.2 1.0 N D:HIS192 4.3 28.1 1.0 CB D:PRO138 4.3 29.2 1.0 CA D:HIS192 4.3 25.1 1.0 C D:HIS192 4.3 32.6 1.0 CG D:ASP140 4.3 26.9 1.0 CB D:VAL139 4.3 27.7 1.0 O39 D:P8V402 4.5 33.9 1.0 C D:VAL139 4.5 28.6 1.0 CB D:ASP140 4.6 29.5 1.0 CG D:ASN137 4.7 30.1 1.0 CA D:ASP140 4.9 29.1 1.0 O D:PRO138 4.9 32.6 1.0 C28 D:P8V402 4.9 33.6 1.0

G.Rai, D.J.Urban, B.T.Mott, X.Hu, S.M.Yang, G.A.Benavides, M.S.Johnson, G.L.Squadrito, K.R.Brimacombe, T.D.Lee, D.M.Cheff, H.Zhu, M.J.Henderson, K.Pohida, G.A.Sulikowski, D.M.Dranow, M.Kabir, P.Shah, E.Padilha, D.Tao, Y.Fang, P.P.Christov, K.Kim, S.Jana, P.Muttil, T.Anderson, N.K.Kunda, H.J.Hathaway, D.F.Kusewitt, N.Oshima, M.Cherukuri, D.R.Davies, J.P.Norenberg, L.A.Sklar, W.J.Moore, C.V.Dang, G.M.Stott, L.Neckers, A.J.Flint, V.M.Darley-Usmar, A.Simeonov, A.G.Waterson, A.Jadhav, M.D.Hall, D.J.Maloney. Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties. J.Med.Chem. V. 63 10984 2020.
ISSN: ISSN 0022-2623
PubMed: 32902275
DOI: 10.1021/ACS.JMEDCHEM.0C00916