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Fluorine in PDB 8u0q: Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series

Enzymatic activity of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series

All present enzymatic activity of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series:
1.8.1.4;

Protein crystallography data

The structure of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series, PDB code: 8u0q was solved by A.A.Dementiev, M.Michino, J.Vendome, J.Ginn, R.Bryk, A.Olland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.53 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.335, 97.928, 123.806, 90, 90, 90
R / Rfree (%) 17.1 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series (pdb code 8u0q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series, PDB code: 8u0q:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8u0q

Go back to Fluorine Binding Sites List in 8u0q
Fluorine binding site 1 out of 4 in the Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:47.3
occ:1.00
 F26 A:U4I502 0.0 47.3 1.0
C25 A:U4I502 1.4 39.9 1.0
F27 A:U4I502 2.2 45.0 1.0
C24 A:U4I502 2.3 30.6 1.0
C28 A:U4I502 2.9 27.0 1.0
CB A:GLU448 3.3 25.8 1.0
C23 A:U4I502 3.4 30.3 1.0
CD A:GLU448 3.5 33.5 1.0
OE2 A:GLU448 3.5 33.2 1.0
O A:HOH633 3.5 41.3 1.0
ND2 A:ASN382 3.7 29.6 1.0
OE1 A:GLU448 3.7 31.4 1.0
CA A:ASN382 4.0 24.2 1.0
CG A:GLU448 4.0 23.8 1.0
O A:ALA381 4.1 28.7 1.0
C19 A:U4I502 4.1 27.2 1.0
CG A:ASN382 4.2 31.9 1.0
N A:ALA383 4.2 26.3 1.0
CB A:ASN382 4.5 22.2 1.0
C21 A:U4I502 4.6 33.0 1.0
CA A:GLU448 4.6 24.7 1.0
C A:GLU448 4.7 27.7 1.0
CZ A:PHE377 4.7 29.6 1.0
C A:ASN382 4.7 23.2 1.0
O A:HOH616 4.8 36.6 1.0
C20 A:U4I502 4.9 30.1 1.0
CE2 A:PHE377 4.9 31.4 1.0
O A:GLU448 4.9 25.7 1.0
N A:ALA449 5.0 22.2 1.0
C A:ALA381 5.0 28.1 1.0
O A:THR445 5.0 24.4 1.0
N A:ASN382 5.0 28.8 1.0
OD1 A:ASN382 5.0 31.7 1.0

Fluorine binding site 2 out of 4 in 8u0q

Go back to Fluorine Binding Sites List in 8u0q
Fluorine binding site 2 out of 4 in the Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:45.0
occ:1.00
 F27 A:U4I502 0.0 45.0 1.0
C25 A:U4I502 1.4 39.9 1.0
F26 A:U4I502 2.2 47.3 1.0
C24 A:U4I502 2.3 30.6 1.0
C28 A:U4I502 2.9 27.0 1.0
CB A:ASN463 3.2 27.4 1.0
C23 A:U4I502 3.4 30.3 1.0
ND2 A:ASN463 3.6 31.6 1.0
CG A:ASN463 3.7 32.0 1.0
CG A:GLU452 3.7 30.5 1.0
CZ A:PHE377 3.8 29.6 1.0
O A:ALA381 3.9 28.7 1.0
OE2 A:GLU452 4.0 42.3 1.0
C19 A:U4I502 4.2 27.2 1.0
CD A:GLU452 4.2 41.6 1.0
O3 A:GOL503 4.4 59.0 1.0
CE1 A:PHE377 4.4 30.1 1.0
OD1 A:ASN463 4.5 32.0 1.0
C21 A:U4I502 4.5 33.0 1.0
CB A:GLU448 4.6 25.8 1.0
CE2 A:PHE377 4.6 31.4 1.0
CA A:ASN463 4.7 27.1 1.0
OE2 A:GLU448 4.7 33.2 1.0
O A:HOH616 4.7 36.6 1.0
C20 A:U4I502 4.9 30.1 1.0
O A:GLU448 4.9 25.7 1.0

Fluorine binding site 3 out of 4 in 8u0q

Go back to Fluorine Binding Sites List in 8u0q
Fluorine binding site 3 out of 4 in the Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F523

b:39.6
occ:1.00
 F26 A:U4I523 0.0 39.6 1.0
C25 A:U4I523 1.4 29.6 1.0
F27 A:U4I523 2.2 39.3 1.0
C24 A:U4I523 2.3 29.5 1.0
C28 A:U4I523 2.9 25.5 1.0
CB B:ASN463 3.2 26.2 1.0
C23 A:U4I523 3.4 25.3 1.0
CG B:ASN463 3.7 36.9 1.0
ND2 B:ASN463 3.7 32.6 1.0
CZ B:PHE377 3.7 29.0 1.0
CG B:GLU452 3.7 30.1 1.0
OE2 B:GLU452 3.8 37.9 1.0
O B:ALA381 3.9 25.7 1.0
C19 A:U4I523 4.1 27.6 1.0
CD B:GLU452 4.1 37.5 1.0
CE2 B:PHE377 4.3 28.2 1.0
CB B:GLU448 4.5 24.2 1.0
OE2 B:GLU448 4.6 29.6 1.0
C21 A:U4I523 4.6 25.7 1.0
OD1 B:ASN463 4.6 31.2 1.0
CE1 B:PHE377 4.6 25.2 1.0
CA B:ASN463 4.7 27.1 1.0
O B:HOH614 4.7 33.4 1.0
C20 A:U4I523 4.9 27.5 1.0
O B:GLU448 4.9 27.1 1.0
CD B:GLU448 5.0 33.6 1.0

Fluorine binding site 4 out of 4 in 8u0q

Go back to Fluorine Binding Sites List in 8u0q
Fluorine binding site 4 out of 4 in the Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of Optimized Analog Tdi-13537 Provided New Insights Into the Potency Determinants of the Sulfonamide Inhibitor Series within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F523

b:39.3
occ:1.00
 F27 A:U4I523 0.0 39.3 1.0
C25 A:U4I523 1.4 29.6 1.0
F26 A:U4I523 2.2 39.6 1.0
C24 A:U4I523 2.4 29.5 1.0
C28 A:U4I523 2.8 25.5 1.0
O B:HOH606 3.1 42.9 1.0
CB B:GLU448 3.4 24.2 1.0
C23 A:U4I523 3.5 25.3 1.0
ND2 B:ASN382 3.5 28.6 1.0
OE2 B:GLU448 3.5 29.6 1.0
CD B:GLU448 3.5 33.6 1.0
OE1 B:GLU448 3.7 31.6 1.0
CA B:ASN382 3.9 21.9 1.0
O B:ALA381 4.0 25.7 1.0
C19 A:U4I523 4.1 27.6 1.0
CG B:GLU448 4.1 24.2 1.0
CG B:ASN382 4.1 27.7 1.0
N B:ALA383 4.1 25.2 1.0
CB B:ASN382 4.4 21.6 1.0
CZ B:PHE377 4.6 29.0 1.0
C B:ASN382 4.6 25.8 1.0
C21 A:U4I523 4.6 25.7 1.0
CA B:GLU448 4.7 22.5 1.0
C B:GLU448 4.7 25.7 1.0
O B:HOH614 4.8 33.4 1.0
C20 A:U4I523 4.9 27.5 1.0
N B:ASN382 4.9 24.9 1.0
C B:ALA381 4.9 26.1 1.0
OD1 B:ASN382 4.9 26.6 1.0
O B:THR445 4.9 22.4 1.0
CE1 B:PHE377 4.9 25.2 1.0
O B:GLU448 5.0 27.1 1.0

Reference:

M.Michino, A.Beautrait, N.A.Boyles, A.Nadupalli, A.Dementiev, S.Sun, J.Ginn, L.Baxt, R.Suto, R.Bryk, S.V.Jerome, D.J.Huggins, J.Vendome. Shape-Based Virtual Screening of A Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors. Acs Bio Med Chem Au V. 3 507 2023.
ISSN: ESSN 2694-2437
PubMed: 38144256
DOI: 10.1021/ACSBIOMEDCHEMAU.3C00046
Page generated: Wed Jul 16 08:53:27 2025

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