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Fluorine in PDB 4j3j: Crystal Structure of Dpp-IV with Compound C3

Enzymatic activity of Crystal Structure of Dpp-IV with Compound C3

All present enzymatic activity of Crystal Structure of Dpp-IV with Compound C3:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Dpp-IV with Compound C3, PDB code: 4j3j was solved by B.Xiong, L.R.Zhu, D.Q.Chen, Y.L.Zhao, F.Jiang, J.K.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 3.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 79.648, 79.648, 292.267, 90.00, 90.00, 120.00
R / Rfree (%) 22.5 / 27

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Dpp-IV with Compound C3 (pdb code 4j3j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Dpp-IV with Compound C3, PDB code: 4j3j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4j3j

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Fluorine binding site 1 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


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 Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:0.3
occ:1.00
 FBB A:D3C801 0.0 0.3 1.0
CBA A:D3C801 1.3 0.1 1.0
FBD A:D3C801 2.2 1.0 1.0
FBC A:D3C801 2.2 0.9 1.0
CAX A:D3C801 2.3 0.0 1.0
OH A:TYR585 2.7 0.8 1.0
NAW A:D3C801 3.0 0.5 1.0
CAT A:D3C801 3.3 0.9 1.0
CE2 A:PHE357 3.4 0.5 1.0
CAY A:D3C801 3.5 0.6 1.0
CD2 A:PHE357 3.7 0.2 1.0
CZ A:TYR585 3.9 0.3 1.0
CAV A:D3C801 4.2 0.9 1.0
CAZ A:D3C801 4.4 0.2 1.0
CE1 A:TYR585 4.4 0.6 1.0
SG A:CYS551 4.5 0.7 1.0
CD A:ARG356 4.5 99.3 1.0
CZ A:PHE357 4.6 0.1 1.0
CAS A:D3C801 4.8 0.0 1.0
O A:CYS551 4.8 93.4 1.0
CE2 A:TYR585 4.8 0.8 1.0
CB A:ARG356 4.9 98.8 1.0

Fluorine binding site 2 out of 12 in 4j3j

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Fluorine binding site 2 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


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 Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:0.9
occ:1.00
 FBC A:D3C801 0.0 0.9 1.0
CBA A:D3C801 1.3 0.1 1.0
FBB A:D3C801 2.2 0.3 1.0
FBD A:D3C801 2.2 1.0 1.0
CAX A:D3C801 2.3 0.0 1.0
NAW A:D3C801 3.1 0.5 1.0
CAY A:D3C801 3.4 0.6 1.0
OH A:TYR585 3.4 0.8 1.0
CAT A:D3C801 3.5 0.9 1.0
CAV A:D3C801 4.2 0.9 1.0
CAZ A:D3C801 4.4 0.2 1.0
CZ A:TYR585 4.6 0.3 1.0
CAS A:D3C801 4.9 0.0 1.0

Fluorine binding site 3 out of 12 in 4j3j

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Fluorine binding site 3 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


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 Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:1.0
occ:1.00
 FBD A:D3C801 0.0 1.0 1.0
CBA A:D3C801 1.3 0.1 1.0
FBB A:D3C801 2.2 0.3 1.0
FBC A:D3C801 2.2 0.9 1.0
CAX A:D3C801 2.4 0.0 1.0
CAY A:D3C801 2.8 0.6 1.0
NAW A:D3C801 3.7 0.5 1.0
CD A:ARG356 3.7 99.3 1.0
OH A:TYR585 3.7 0.8 1.0
CAZ A:D3C801 4.1 0.2 1.0
CB A:ARG356 4.3 98.8 1.0
CAV A:D3C801 4.5 0.9 1.0
CD2 A:PHE357 4.5 0.2 1.0
CG A:ARG356 4.5 98.9 1.0
CE1 A:TYR585 4.6 0.6 1.0
NH1 A:ARG356 4.6 1.0 1.0
CAT A:D3C801 4.6 0.9 1.0
CZ A:TYR585 4.6 0.3 1.0
NE A:ARG356 4.8 0.1 1.0
CE2 A:PHE357 4.8 0.5 1.0

Fluorine binding site 4 out of 12 in 4j3j

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Fluorine binding site 4 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


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 Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:89.8
occ:1.00
 FAI A:D3C801 0.0 89.8 1.0
CAB A:D3C801 1.3 90.6 1.0
CAA A:D3C801 2.4 89.4 1.0
CAC A:D3C801 2.4 94.0 1.0
FAH A:D3C801 2.7 86.1 1.0
CD2 A:TYR631 3.3 90.7 1.0
CE1 A:TYR666 3.5 94.0 1.0
CB A:TYR631 3.6 89.1 1.0
CAF A:D3C801 3.6 92.2 1.0
CAD A:D3C801 3.6 95.8 1.0
OH A:TYR666 3.7 94.6 1.0
CZ A:TYR666 3.7 95.1 1.0
CH2 A:TRP659 3.9 91.0 1.0
CG A:TYR631 3.9 89.4 1.0
CA A:TYR631 4.1 88.8 1.0
CAE A:D3C801 4.1 94.9 1.0
N A:TYR631 4.2 88.8 1.0
CZ3 A:TRP659 4.2 91.3 1.0
OG A:SER630 4.3 93.9 1.0
CD1 A:TYR666 4.3 93.2 1.0
CE2 A:TYR631 4.3 91.8 1.0
CG2 A:VAL656 4.4 83.4 1.0
CE2 A:TYR662 4.5 81.8 1.0
CE2 A:TYR666 4.7 95.9 1.0
CZ A:TYR662 4.8 80.8 1.0
CAJ A:D3C801 4.9 0.8 1.0
CD2 A:TYR662 4.9 82.5 1.0
OH A:TYR547 4.9 0.8 1.0
C A:SER630 4.9 88.7 1.0

Fluorine binding site 5 out of 12 in 4j3j

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Fluorine binding site 5 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


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 Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:86.1
occ:1.00
 FAH A:D3C801 0.0 86.1 1.0
CAA A:D3C801 1.3 89.4 1.0
CAB A:D3C801 2.4 90.6 1.0
CAF A:D3C801 2.4 92.2 1.0
FAI A:D3C801 2.7 89.8 1.0
CG2 A:VAL656 3.0 83.4 1.0
CG2 A:VAL711 3.2 79.3 1.0
CAC A:D3C801 3.6 94.0 1.0
CAE A:D3C801 3.6 94.9 1.0
OG A:SER630 3.7 93.9 1.0
CE1 A:TYR662 3.8 79.3 1.0
CZ A:TYR662 3.9 80.8 1.0
CD1 A:TYR662 4.1 81.5 1.0
CAD A:D3C801 4.1 95.8 1.0
CE2 A:TYR662 4.3 81.8 1.0
C A:SER630 4.3 88.7 1.0
OH A:TYR662 4.4 80.4 1.0
N A:TYR631 4.4 88.8 1.0
CG A:TYR662 4.5 83.4 1.0
CB A:VAL656 4.5 82.9 1.0
CB A:VAL711 4.5 80.7 1.0
O A:SER630 4.6 86.8 1.0
CD2 A:TYR662 4.6 82.5 1.0
CA A:SER630 4.7 89.9 1.0
FAG A:D3C801 4.7 96.2 1.0
CG1 A:VAL711 4.8 80.1 1.0
CB A:SER630 4.8 92.8 1.0
CA A:TYR631 4.8 88.8 1.0
NE2 A:HIS740 5.0 91.5 1.0

Fluorine binding site 6 out of 12 in 4j3j

Go back to Fluorine Binding Sites List in 4j3j
Fluorine binding site 6 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


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 Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:96.2
occ:1.00
 FAG A:D3C801 0.0 96.2 1.0
CAE A:D3C801 1.3 94.9 1.0
CAD A:D3C801 2.4 95.8 1.0
CAF A:D3C801 2.4 92.2 1.0
ND2 A:ASN710 2.8 77.6 1.0
CAJ A:D3C801 2.9 0.8 1.0
OE2 A:GLU205 3.2 85.2 1.0
NH2 A:ARG125 3.2 91.3 1.0
CG A:ASN710 3.4 76.4 1.0
OH A:TYR662 3.4 80.4 1.0
OD1 A:ASN710 3.5 76.9 1.0
NAM A:D3C801 3.6 0.8 1.0
CAC A:D3C801 3.6 94.0 1.0
CAA A:D3C801 3.6 89.4 1.0
CD2 A:HIS740 3.9 90.9 1.0
CAK A:D3C801 3.9 0.0 1.0
NE2 A:HIS740 3.9 91.5 1.0
OG A:SER630 4.0 93.9 1.0
CAB A:D3C801 4.1 90.6 1.0
CD A:GLU205 4.4 88.6 1.0
CZ A:TYR662 4.5 80.8 1.0
CZ A:ARG125 4.5 92.5 1.0
CB A:ASN710 4.7 76.0 1.0
FAH A:D3C801 4.7 86.1 1.0
CAL A:D3C801 4.9 0.4 1.0
CG A:HIS740 4.9 88.5 1.0
CE1 A:HIS740 5.0 92.0 1.0

Fluorine binding site 7 out of 12 in 4j3j

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Fluorine binding site 7 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.4
occ:1.00
 FBB B:D3C801 0.0 0.4 1.0
CBA B:D3C801 1.3 1.0 1.0
FBD B:D3C801 2.2 0.5 1.0
FBC B:D3C801 2.2 0.5 1.0
CAX B:D3C801 2.3 0.9 1.0
NAW B:D3C801 3.0 0.9 1.0
OH B:TYR585 3.0 0.3 1.0
CE2 B:PHE357 3.2 0.7 1.0
CAT B:D3C801 3.4 0.7 1.0
CAY B:D3C801 3.4 0.3 1.0
CD2 B:PHE357 3.5 0.7 1.0
CZ B:TYR585 4.1 0.1 1.0
CAV B:D3C801 4.2 0.1 1.0
CAZ B:D3C801 4.4 0.6 1.0
SG B:CYS551 4.4 0.5 1.0
CD B:ARG356 4.5 0.4 1.0
CZ B:PHE357 4.5 0.8 1.0
CAS B:D3C801 4.7 0.7 1.0
CB B:ARG356 4.7 0.5 1.0
CE1 B:TYR585 4.7 0.4 1.0
O B:CYS551 4.7 0.4 1.0
CG B:PHE357 4.8 0.5 1.0
CE2 B:TYR585 4.9 0.7 1.0

Fluorine binding site 8 out of 12 in 4j3j

Go back to Fluorine Binding Sites List in 4j3j
Fluorine binding site 8 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.5
occ:1.00
 FBC B:D3C801 0.0 0.5 1.0
CBA B:D3C801 1.3 1.0 1.0
FBD B:D3C801 2.2 0.5 1.0
FBB B:D3C801 2.2 0.4 1.0
CAX B:D3C801 2.3 0.9 1.0
NAW B:D3C801 3.0 0.9 1.0
OH B:TYR585 3.2 0.3 1.0
CAT B:D3C801 3.4 0.7 1.0
CAY B:D3C801 3.4 0.3 1.0
CAV B:D3C801 4.2 0.1 1.0
CAZ B:D3C801 4.4 0.6 1.0
CZ B:TYR585 4.5 0.1 1.0
CAS B:D3C801 4.9 0.7 1.0

Fluorine binding site 9 out of 12 in 4j3j

Go back to Fluorine Binding Sites List in 4j3j
Fluorine binding site 9 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.5
occ:1.00
 FBD B:D3C801 0.0 0.5 1.0
CBA B:D3C801 1.3 1.0 1.0
FBB B:D3C801 2.2 0.4 1.0
FBC B:D3C801 2.2 0.5 1.0
CAX B:D3C801 2.3 0.9 1.0
CAY B:D3C801 2.8 0.3 1.0
NAW B:D3C801 3.7 0.9 1.0
OH B:TYR585 3.9 0.3 1.0
CD B:ARG356 3.9 0.4 1.0
CAZ B:D3C801 4.1 0.6 1.0
CB B:ARG356 4.3 0.5 1.0
CAV B:D3C801 4.5 0.1 1.0
CD2 B:PHE357 4.5 0.7 1.0
CAT B:D3C801 4.6 0.7 1.0
CG B:ARG356 4.6 0.1 1.0
NH1 B:ARG356 4.7 0.2 1.0
CZ B:TYR585 4.8 0.1 1.0
CE1 B:TYR585 4.9 0.4 1.0
CE2 B:PHE357 4.9 0.7 1.0

Fluorine binding site 10 out of 12 in 4j3j

Go back to Fluorine Binding Sites List in 4j3j
Fluorine binding site 10 out of 12 in the Crystal Structure of Dpp-IV with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Dpp-IV with Compound C3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:85.2
occ:1.00
 FAI B:D3C801 0.0 85.2 1.0
CAB B:D3C801 1.3 84.3 1.0
CAA B:D3C801 2.4 83.7 1.0
CAC B:D3C801 2.4 85.8 1.0
FAH B:D3C801 2.7 82.4 1.0
CD2 B:TYR631 3.1 98.4 1.0
CE1 B:TYR666 3.5 94.0 1.0
CB B:TYR631 3.6 95.4 1.0
CAF B:D3C801 3.6 84.5 1.0
CAD B:D3C801 3.7 87.3 1.0
CH2 B:TRP659 3.7 92.3 1.0
CG B:TYR631 3.8 98.0 1.0
OH B:TYR666 3.8 93.5 1.0
CZ B:TYR666 3.9 94.6 1.0
CA B:TYR631 3.9 93.2 1.0
CAE B:D3C801 4.1 86.4 1.0
CZ3 B:TRP659 4.1 92.4 1.0
CG2 B:VAL656 4.2 80.5 1.0
N B:TYR631 4.2 94.7 1.0
CE2 B:TYR631 4.2 99.1 1.0
OG B:SER630 4.3 97.1 1.0
CD1 B:TYR666 4.3 93.8 1.0
CE2 B:TYR662 4.5 72.8 1.0
CD2 B:TYR662 4.8 73.0 1.0
CE2 B:TYR666 4.8 96.2 1.0
C B:SER630 4.8 95.5 1.0
CZ B:TYR662 4.9 72.6 1.0
CAJ B:D3C801 4.9 90.7 1.0
CZ2 B:TRP659 4.9 91.7 1.0

Reference:

L.Zhu, Y.Li, L.Qiu, M.Su, X.Wang, C.Xia, Y.Qu, J.Li, J.Li, B.Xiong, J.Shen. Design and Synthesis of 4-(2,4,5-Trifluorophenyl)Butane-1,3-Diamines As Dipeptidyl Peptidase IV Inhibitors Chemmedchem V. 8 1104 2013.
ISSN: ISSN 1860-7179
PubMed: 23671024
DOI: 10.1002/CMDC.201300104
Page generated: Thu Aug 1 02:46:48 2024

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