Fluorine in PDB 5w8i: Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc

Enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc

All present enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc, PDB code: 5w8i was solved by C.M.Lukacs, J.Abendroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.840, 80.430, 119.620, 90.00, 117.73, 90.00
R / Rfree (%) 14.9 / 18.8

Other elements in 5w8i:

The structure of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc (pdb code 5w8i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc, PDB code: 5w8i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5w8i

Go back to Fluorine Binding Sites List in 5w8i
Fluorine binding site 1 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


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 Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:32.1
occ:1.00
F1 A:9YD403 0.0 32.1 1.0
C2 A:9YD403 1.4 32.8 1.0
C3 A:9YD403 2.3 34.0 1.0
C7 A:9YD403 2.4 30.2 1.0
F8 A:9YD403 2.6 41.9 1.0
CD A:GLN99 3.1 32.4 1.0
CG A:LEU108 3.1 24.6 1.0
OE1 A:GLN99 3.2 32.3 1.0
CD1 A:LEU108 3.3 25.2 1.0
CB A:LEU108 3.4 24.0 1.0
NE2 A:GLN99 3.6 34.3 1.0
CG A:GLN99 3.6 32.3 1.0
C4 A:9YD403 3.6 31.6 1.0
CB A:GLN99 3.7 31.2 1.0
C6 A:9YD403 3.7 28.8 1.0
CA A:ARG105 4.0 32.6 1.0
C5 A:9YD403 4.1 27.9 1.0
CG A:ARG105 4.2 43.1 1.0
CB A:ARG105 4.5 37.0 1.0
O A:ARG105 4.5 28.4 1.0
CD2 A:LEU108 4.5 24.7 1.0
CA A:GLN99 4.6 29.8 1.0
O A:HOH586 4.7 41.9 1.0
CD A:PRO138 4.8 21.4 1.0
C A:ARG105 4.8 29.5 1.0
O A:SER104 4.8 27.1 1.0
N A:ARG105 4.8 31.4 1.0
CA A:LEU108 4.8 22.9 1.0

Fluorine binding site 2 out of 6 in 5w8i

Go back to Fluorine Binding Sites List in 5w8i
Fluorine binding site 2 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


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 Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:41.9
occ:1.00
F8 A:9YD403 0.0 41.9 1.0
C3 A:9YD403 1.3 34.0 1.0
C2 A:9YD403 2.3 32.8 1.0
C4 A:9YD403 2.4 31.6 1.0
F1 A:9YD403 2.6 32.1 1.0
CG A:ARG105 3.2 43.1 1.0
CD A:ARG105 3.4 49.5 1.0
OE1 A:GLN99 3.6 32.3 1.0
C7 A:9YD403 3.6 30.2 1.0
C5 A:9YD403 3.6 27.9 1.0
NE A:ARG105 3.7 56.7 1.0
CB A:ARG105 3.8 37.0 1.0
CD A:GLN99 4.0 32.4 1.0
NE2 A:GLN99 4.1 34.3 1.0
C6 A:9YD403 4.1 28.8 1.0
CA A:ARG105 4.2 32.6 1.0
O A:HOH692 4.7 37.6 1.0
CZ A:ARG105 4.8 66.1 1.0
C9 A:9YD403 4.8 25.6 1.0
CG A:PRO138 5.0 21.0 1.0
O A:HOH586 5.0 41.9 1.0

Fluorine binding site 3 out of 6 in 5w8i

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Fluorine binding site 3 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


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 Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:27.5
occ:1.00
F1 C:9YD402 0.0 27.5 1.0
C2 C:9YD402 1.3 28.3 1.0
C7 C:9YD402 2.3 26.2 1.0
C3 C:9YD402 2.4 28.8 1.0
F8 C:9YD402 2.8 33.0 1.0
CG C:LEU108 3.2 19.0 1.0
OE1 C:GLN99 3.3 28.1 1.0
CD1 C:LEU108 3.3 18.9 1.0
CD C:GLN99 3.3 26.4 1.0
CB C:LEU108 3.5 18.8 1.0
CB C:GLN99 3.6 24.4 1.0
C6 C:9YD402 3.6 24.7 1.0
C4 C:9YD402 3.7 26.3 1.0
CG C:GLN99 3.7 25.1 1.0
NE2 C:GLN99 3.8 25.8 1.0
CG C:ARG105 4.1 41.0 1.0
C5 C:9YD402 4.1 24.3 1.0
CA C:ARG105 4.2 29.1 1.0
CG C:PRO138 4.6 22.3 1.0
O C:ARG105 4.6 23.8 1.0
CA C:GLN99 4.6 24.5 1.0
CB C:ARG105 4.6 34.9 1.0
CD2 C:LEU108 4.6 18.7 1.0
O C:HOH557 4.7 34.3 1.0
CD C:PRO138 4.8 22.4 1.0
C C:ARG105 4.9 25.2 1.0
O C:SER104 4.9 21.7 1.0
CA C:LEU108 5.0 18.7 1.0
N C:ARG105 5.0 28.1 1.0

Fluorine binding site 4 out of 6 in 5w8i

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Fluorine binding site 4 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


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 Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:33.0
occ:1.00
F8 C:9YD402 0.0 33.0 1.0
C3 C:9YD402 1.4 28.8 1.0
C4 C:9YD402 2.4 26.3 1.0
C2 C:9YD402 2.4 28.3 1.0
F1 C:9YD402 2.8 27.5 1.0
CG C:ARG105 3.0 41.0 1.0
CD C:ARG105 3.2 47.5 1.0
NE C:ARG105 3.4 56.6 1.0
C5 C:9YD402 3.7 24.3 1.0
C7 C:9YD402 3.7 26.2 1.0
OE1 C:GLN99 3.8 28.1 1.0
CB C:ARG105 4.0 34.9 1.0
O C:HOH618 4.1 36.9 1.0
C6 C:9YD402 4.1 24.7 1.0
CD C:GLN99 4.3 26.4 1.0
NE2 C:GLN99 4.4 25.8 1.0
CG C:PRO138 4.4 22.3 1.0
O C:HOH681 4.5 38.5 1.0
CA C:ARG105 4.5 29.1 1.0
CZ C:ARG105 4.6 59.0 1.0
CB C:PRO138 4.9 20.9 1.0
C9 C:9YD402 4.9 22.6 1.0

Fluorine binding site 5 out of 6 in 5w8i

Go back to Fluorine Binding Sites List in 5w8i
Fluorine binding site 5 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:33.9
occ:1.00
F1 D:9YD403 0.0 33.9 1.0
C2 D:9YD403 1.4 31.2 1.0
C3 D:9YD403 2.4 29.4 1.0
C7 D:9YD403 2.4 29.1 1.0
F8 D:9YD403 2.7 34.3 1.0
O D:HOH640 3.3 42.0 1.0
CB D:GLN99 3.3 32.8 1.0
CD1 D:LEU108 3.3 25.3 1.0
CG D:LEU108 3.3 24.0 1.0
N D:GLN99 3.3 28.9 1.0
O D:HOH555 3.4 24.4 1.0
CD2 D:LEU108 3.5 25.5 1.0
C6 D:9YD403 3.6 26.4 1.0
C4 D:9YD403 3.6 26.2 1.0
CA D:GLN99 3.7 29.9 1.0
O D:HOH685 3.8 43.8 1.0
O D:ALA97 3.9 23.3 1.0
C5 D:9YD403 4.0 23.9 1.0
C D:ARG98 4.1 27.3 1.0
OE1 D:GLN99 4.3 39.7 1.0
CG D:GLN99 4.4 35.3 1.0
CA D:ARG98 4.4 28.2 1.0
C D:ALA97 4.6 26.2 1.0
CD D:GLN99 4.7 37.5 1.0
CD D:PRO138 4.8 16.2 1.0
CB D:LEU108 4.8 23.2 1.0
O D:ASN137 4.9 16.5 1.0
N D:ARG98 4.9 28.3 1.0
O D:ARG98 5.0 25.7 1.0

Fluorine binding site 6 out of 6 in 5w8i

Go back to Fluorine Binding Sites List in 5w8i
Fluorine binding site 6 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:34.3
occ:1.00
F8 D:9YD403 0.0 34.3 1.0
C3 D:9YD403 1.3 29.4 1.0
C2 D:9YD403 2.3 31.2 1.0
C4 D:9YD403 2.4 26.2 1.0
F1 D:9YD403 2.7 33.9 1.0
OE1 D:GLN99 3.4 39.7 1.0
O D:HOH685 3.5 43.8 1.0
C5 D:9YD403 3.6 23.9 1.0
C7 D:9YD403 3.6 29.1 1.0
CD1 D:LEU108 3.8 25.3 1.0
C6 D:9YD403 4.1 26.4 1.0
CG D:LEU108 4.2 24.0 1.0
CD D:GLN99 4.3 37.5 1.0
CD D:PRO138 4.3 16.2 1.0
CB D:GLN99 4.3 32.8 1.0
CG D:PRO138 4.4 16.1 1.0
O D:HOH640 4.7 42.0 1.0
CG D:GLN99 4.8 35.3 1.0
CB D:PRO138 4.8 15.8 1.0
C9 D:9YD403 4.8 20.3 1.0

Reference:

G.Rai, K.R.Brimacombe, B.T.Mott, D.J.Urban, X.Hu, S.M.Yang, T.D.Lee, D.M.Cheff, J.Kouznetsova, G.A.Benavides, K.Pohida, E.J.Kuenstner, D.K.Luci, C.M.Lukacs, D.R.Davies, D.M.Dranow, H.Zhu, G.Sulikowski, W.J.Moore, G.M.Stott, A.J.Flint, M.D.Hall, V.M.Darley-Usmar, L.M.Neckers, C.V.Dang, A.G.Waterson, A.Simeonov, A.Jadhav, D.J.Maloney. Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (Ldh). J. Med. Chem. V. 60 9184 2017.
ISSN: ISSN 1520-4804
PubMed: 29120638
DOI: 10.1021/ACS.JMEDCHEM.7B00941
Page generated: Sun Dec 13 12:41:31 2020

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