Fluorine in PDB 5w8k: Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh

Enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh

All present enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh, PDB code: 5w8k was solved by C.M.Lukacs, D.M.Dranow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.18 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.760, 81.080, 120.440, 90.00, 117.14, 90.00
R / Rfree (%) 13.8 / 16.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh (pdb code 5w8k). 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 29 and Nadh, PDB code: 5w8k:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5w8k

Go back to Fluorine Binding Sites List in 5w8k
Fluorine binding site 1 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh


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 29 and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:31.0
occ:0.81
 F20 A:9Y7501 0.0 31.0 0.8
C19 A:9Y7501 1.4 30.5 0.8
C18 A:9Y7501 2.4 27.2 0.8
C21 A:9Y7501 2.5 31.5 0.8
F23 A:9Y7501 2.9 35.6 0.8
C17 A:9Y7501 3.6 30.7 0.8
C22 A:9Y7501 3.7 30.1 0.8
N A:VAL109 3.8 34.3 1.0
CD A:PRO138 3.8 16.8 1.0
CB A:LEU108 3.9 32.4 1.0
C A:LEU108 3.9 35.9 1.0
O A:ASN137 4.0 14.8 1.0
O A:LEU108 4.1 34.4 1.0
CA A:VAL109 4.2 27.6 1.0
C16 A:9Y7501 4.2 29.5 0.8
CG2 A:VAL109 4.3 30.2 1.0
ND2 A:ASN112 4.3 24.5 1.0
N A:PRO138 4.5 14.9 1.0
C A:ASN137 4.5 14.5 1.0
CA A:LEU108 4.5 35.9 1.0
CB A:VAL109 4.9 28.4 1.0
O A:ALA97 4.9 29.4 1.0
CG A:PRO138 5.0 17.7 1.0

Fluorine binding site 2 out of 6 in 5w8k

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Fluorine binding site 2 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh


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 29 and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.6
occ:0.81
 F23 A:9Y7501 0.0 35.6 0.8
C21 A:9Y7501 1.4 31.5 0.8
C22 A:9Y7501 2.3 30.1 0.8
C19 A:9Y7501 2.5 30.5 0.8
F20 A:9Y7501 2.9 31.0 0.8
CD A:PRO138 3.3 16.8 1.0
CG2 A:VAL109 3.5 30.2 1.0
C16 A:9Y7501 3.6 29.5 0.8
CG A:PRO138 3.7 17.7 1.0
C18 A:9Y7501 3.7 27.2 0.8
CB A:PRO138 3.7 16.6 1.0
C17 A:9Y7501 4.1 30.7 0.8
N A:PRO138 4.1 14.9 1.0
CA A:PRO138 4.5 15.1 1.0
C32 A:9Y7501 4.7 28.0 0.8
CB A:VAL109 4.8 28.4 1.0
C15 A:9Y7501 4.9 27.8 0.8
C A:ASN137 4.9 14.5 1.0
N A:VAL109 4.9 34.3 1.0
CA A:VAL109 5.0 27.6 1.0

Fluorine binding site 3 out of 6 in 5w8k

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Fluorine binding site 3 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh


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 29 and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:35.2
occ:1.00
 F20 C:9Y7501 0.0 35.2 1.0
C19 C:9Y7501 1.4 27.3 1.0
C21 C:9Y7501 2.4 24.2 1.0
C18 C:9Y7501 2.4 26.1 1.0
F23 C:9Y7501 2.8 27.2 1.0
CG C:LEU108 3.1 21.0 1.0
CD2 C:LEU108 3.3 21.6 1.0
CD C:PRO138 3.6 15.2 1.0
C17 C:9Y7501 3.6 24.5 1.0
C22 C:9Y7501 3.6 21.3 1.0
ND2 C:ASN112 3.7 23.4 1.0
CB C:LEU108 3.8 20.3 1.0
CG2 C:VAL109 3.8 18.5 1.0
N C:VAL109 3.9 18.2 1.0
C C:LEU108 4.0 17.4 1.0
C16 C:9Y7501 4.1 20.7 1.0
CA C:VAL109 4.1 17.6 1.0
O C:ASN137 4.3 14.8 1.0
O C:LEU108 4.3 17.7 1.0
CD1 C:LEU108 4.3 21.7 1.0
N C:PRO138 4.4 14.3 1.0
CG C:PRO138 4.5 14.8 1.0
CA C:LEU108 4.5 19.1 1.0
O C:HOH651 4.6 26.2 1.0
C C:ASN137 4.6 14.2 1.0
CB C:VAL109 4.6 18.3 1.0
O C:ARG105 4.6 21.8 1.0
CG C:ASN112 4.9 21.1 1.0
CB C:PRO138 5.0 14.9 1.0

Fluorine binding site 4 out of 6 in 5w8k

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Fluorine binding site 4 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh


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 29 and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:27.2
occ:1.00
 F23 C:9Y7501 0.0 27.2 1.0
C21 C:9Y7501 1.3 24.2 1.0
C22 C:9Y7501 2.3 21.3 1.0
C19 C:9Y7501 2.4 27.3 1.0
F20 C:9Y7501 2.8 35.2 1.0
CG2 C:VAL109 3.5 18.5 1.0
C16 C:9Y7501 3.5 20.7 1.0
CB C:PRO138 3.6 14.9 1.0
C18 C:9Y7501 3.7 26.1 1.0
CG C:PRO138 3.8 14.8 1.0
CD C:PRO138 3.8 15.2 1.0
C17 C:9Y7501 4.1 24.5 1.0
N C:PRO138 4.4 14.3 1.0
C32 C:9Y7501 4.5 21.0 1.0
CA C:PRO138 4.5 14.5 1.0
C08 C:9Y7501 4.7 19.2 1.0
C15 C:9Y7501 4.8 17.2 1.0
C33 C:9Y7501 4.8 19.6 1.0
CB C:VAL109 4.9 18.3 1.0
O C:ARG105 5.0 21.8 1.0

Fluorine binding site 5 out of 6 in 5w8k

Go back to Fluorine Binding Sites List in 5w8k
Fluorine binding site 5 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh


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 29 and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:53.0
occ:0.76
 F20 D:9Y7501 0.0 53.0 0.8
C19 D:9Y7501 1.4 46.4 0.8
C21 D:9Y7501 2.3 44.3 0.8
C18 D:9Y7501 2.4 43.9 0.8
CD1 D:LEU108 2.7 28.6 1.0
F23 D:9Y7501 2.7 49.4 0.8
CG D:LEU108 2.7 26.9 1.0
OE1 D:GLN99 3.0 47.4 1.0
CD D:GLN99 3.4 46.1 1.0
CB D:LEU108 3.4 25.4 1.0
C22 D:9Y7501 3.6 40.6 0.8
CB D:GLN99 3.6 43.2 1.0
C17 D:9Y7501 3.7 38.3 0.8
CG D:GLN99 3.9 44.8 1.0
CD2 D:LEU108 4.0 27.2 1.0
NE2 D:GLN99 4.0 48.1 1.0
C16 D:9Y7501 4.1 36.0 0.8
CD D:PRO138 4.3 14.6 1.0
CA D:GLN99 4.4 40.6 1.0
CG D:PRO138 4.5 15.1 1.0
N D:GLN99 4.6 39.2 1.0
CA D:LEU108 4.8 22.5 1.0

Fluorine binding site 6 out of 6 in 5w8k

Go back to Fluorine Binding Sites List in 5w8k
Fluorine binding site 6 out of 6 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 and Nadh


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 29 and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:49.4
occ:0.76
 F23 D:9Y7501 0.0 49.4 0.8
C21 D:9Y7501 1.4 44.3 0.8
C22 D:9Y7501 2.4 40.6 0.8
C19 D:9Y7501 2.4 46.4 0.8
F20 D:9Y7501 2.7 53.0 0.8
OE1 D:GLN99 3.3 47.4 1.0
C16 D:9Y7501 3.7 36.0 0.8
C18 D:9Y7501 3.7 43.9 0.8
CD D:GLN99 4.1 46.1 1.0
C17 D:9Y7501 4.2 38.3 0.8
NE2 D:GLN99 4.3 48.1 1.0
C32 D:9Y7501 4.3 25.1 0.8
CB D:ARG105 4.4 30.6 1.0
CG D:PRO138 4.4 15.1 1.0
CB D:PRO138 4.6 14.5 1.0
C33 D:9Y7501 4.6 25.2 0.8
CA D:ARG105 4.7 28.1 1.0
C08 D:9Y7501 4.8 26.4 0.8
C15 D:9Y7501 4.9 28.9 0.8
CD1 D:LEU108 5.0 28.6 1.0
CD D:PRO138 5.0 14.6 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 12:41:33 2020

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