Atomistry » Fluorine » PDB 5uv3-5vd4 » 5v7i
Atomistry »
  Fluorine »
    PDB 5uv3-5vd4 »
      5v7i »

Fluorine in PDB 5v7i: Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile

Enzymatic activity of Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile

All present enzymatic activity of Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile:
2.1.2.1;

Protein crystallography data

The structure of Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile, PDB code: 5v7i was solved by G.S.Ducker, J.M.Ghergurovich, N.Mainolfi, V.Suri, S.Jeong, A.Friedman, M.Manfredi, H.Kim, J.D.Rabinowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.00 / 2.47
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 160.140, 160.140, 210.100, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile (pdb code 5v7i). 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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile, PDB code: 5v7i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5v7i

Go back to Fluorine Binding Sites List in 5v7i
Fluorine binding site 1 out of 6 in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile


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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.0
occ:1.00
 FAI A:8Z1601 0.0 0.0 1.0
CAG A:8Z1601 1.4 0.3 1.0
FAH A:8Z1601 2.2 0.2 1.0
FAJ A:8Z1601 2.2 0.8 1.0
CAF A:8Z1601 2.3 99.5 1.0
CAB A:8Z1601 2.7 97.0 1.0
O A:HOH962 3.3 48.3 1.0
CAE A:8Z1601 3.6 0.3 1.0
NZ A:LYS409 4.0 56.8 1.0
CE A:LYS409 4.0 56.0 1.0
CAA A:8Z1601 4.1 94.7 1.0
CG B:TYR105 4.8 59.6 1.0
CAD A:8Z1601 4.8 0.2 1.0
CD1 B:TYR105 4.9 62.0 1.0
NBA A:8Z1601 4.9 87.7 1.0
CD2 B:TYR105 4.9 63.2 1.0
CAC A:8Z1601 4.9 97.5 1.0

Fluorine binding site 2 out of 6 in 5v7i

Go back to Fluorine Binding Sites List in 5v7i
Fluorine binding site 2 out of 6 in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile


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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.8
occ:1.00
 FAJ A:8Z1601 0.0 0.8 1.0
CAG A:8Z1601 1.4 0.3 1.0
FAI A:8Z1601 2.2 0.0 1.0
FAH A:8Z1601 2.2 0.2 1.0
CAF A:8Z1601 2.3 99.5 1.0
CAE A:8Z1601 2.8 0.3 1.0
NZ A:LYS409 3.4 56.8 1.0
CAB A:8Z1601 3.6 97.0 1.0
CE A:LYS409 3.8 56.0 1.0
CG A:LYS409 4.1 53.5 1.0
O B:TYR105 4.1 56.5 1.0
CAD A:8Z1601 4.1 0.2 1.0
O A:LYS409 4.3 51.8 1.0
CAR A:8Z1601 4.4 0.7 1.0
CB B:TYR105 4.6 55.8 1.0
CD A:LYS409 4.6 54.8 1.0
CAA A:8Z1601 4.7 94.7 1.0
NAU A:8Z1601 4.8 0.7 1.0
CAQ A:8Z1601 4.8 0.3 1.0
CG B:TYR105 4.8 59.6 1.0
CA B:TYR105 4.8 54.6 1.0
C B:TYR105 4.8 55.4 1.0
O A:HOH962 4.9 48.3 1.0
CAC A:8Z1601 4.9 97.5 1.0
CAT A:8Z1601 5.0 0.7 1.0
CD2 B:TYR105 5.0 63.2 1.0

Fluorine binding site 3 out of 6 in 5v7i

Go back to Fluorine Binding Sites List in 5v7i
Fluorine binding site 3 out of 6 in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile


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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.2
occ:1.00
 FAH A:8Z1601 0.0 0.2 1.0
CAG A:8Z1601 1.4 0.3 1.0
FAI A:8Z1601 2.2 0.0 1.0
FAJ A:8Z1601 2.2 0.8 1.0
CAF A:8Z1601 2.3 99.5 1.0
CAE A:8Z1601 3.1 0.3 1.0
CAB A:8Z1601 3.1 97.0 1.0
CE A:LYS409 4.0 56.0 1.0
NAU A:8Z1601 4.0 0.7 1.0
CG A:LYS409 4.2 53.5 1.0
CAA A:8Z1601 4.4 94.7 1.0
CAD A:8Z1601 4.4 0.2 1.0
O A:HOH962 4.4 48.3 1.0
NZ A:LYS409 4.5 56.8 1.0
CAT A:8Z1601 4.6 0.7 1.0
CD A:LYS409 4.6 54.8 1.0
O A:LYS409 4.7 51.8 1.0
CAC A:8Z1601 4.8 97.5 1.0

Fluorine binding site 4 out of 6 in 5v7i

Go back to Fluorine Binding Sites List in 5v7i
Fluorine binding site 4 out of 6 in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile


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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:0.6
occ:1.00
 FAI B:8Z1601 0.0 0.6 1.0
CAG B:8Z1601 1.4 0.1 1.0
FAJ B:8Z1601 2.2 0.1 1.0
FAH B:8Z1601 2.2 0.9 1.0
CAF B:8Z1601 2.3 0.9 1.0
CAB B:8Z1601 2.7 0.2 1.0
CAE B:8Z1601 3.6 0.4 1.0
CE B:LYS409 3.8 72.5 1.0
CAA B:8Z1601 4.1 0.7 1.0
NZ B:LYS409 4.6 72.5 1.0
CD2 A:TYR105 4.7 76.0 1.0
CAD B:8Z1601 4.8 0.6 1.0
CE2 A:TYR105 4.9 78.5 1.0
CD B:LYS409 4.9 71.4 1.0
NBA B:8Z1601 4.9 0.3 1.0
CAC B:8Z1601 4.9 0.6 1.0
CG A:TYR105 5.0 73.4 1.0

Fluorine binding site 5 out of 6 in 5v7i

Go back to Fluorine Binding Sites List in 5v7i
Fluorine binding site 5 out of 6 in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile


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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:0.1
occ:1.00
 FAJ B:8Z1601 0.0 0.1 1.0
CAG B:8Z1601 1.4 0.1 1.0
FAI B:8Z1601 2.2 0.6 1.0
FAH B:8Z1601 2.2 0.9 1.0
CAF B:8Z1601 2.3 0.9 1.0
CAE B:8Z1601 2.7 0.4 1.0
CE B:LYS409 3.2 72.5 1.0
CAB B:8Z1601 3.6 0.2 1.0
CG B:LYS409 3.7 70.4 1.0
CD B:LYS409 4.0 71.4 1.0
O A:TYR105 4.1 71.6 1.0
CAD B:8Z1601 4.1 0.6 1.0
NZ B:LYS409 4.3 72.5 1.0
CAR B:8Z1601 4.4 0.1 1.0
O B:LYS409 4.6 66.7 1.0
CAA B:8Z1601 4.7 0.7 1.0
NAU B:8Z1601 4.7 0.4 1.0
CB A:TYR105 4.8 69.5 1.0
CD2 A:TYR105 4.8 76.0 1.0
CAQ B:8Z1601 4.8 0.7 1.0
CA A:TYR105 4.9 66.9 1.0
C A:TYR105 4.9 68.5 1.0
CAC B:8Z1601 4.9 0.6 1.0
CAT B:8Z1601 4.9 0.4 1.0
CG A:TYR105 4.9 73.4 1.0

Fluorine binding site 6 out of 6 in 5v7i

Go back to Fluorine Binding Sites List in 5v7i
Fluorine binding site 6 out of 6 in the Crystal Structure of Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile


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 Homo Sapiens Serine Hydroxymethyltransferase 2 (Mitochondrial) (SHMT2), in Complex with Glycine, Plp and Folate- Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3-Methyl-4- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydropyrano[2, 3-C]Pyrazole-5-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:0.9
occ:1.00
 FAH B:8Z1601 0.0 0.9 1.0
CAG B:8Z1601 1.4 0.1 1.0
FAJ B:8Z1601 2.2 0.1 1.0
FAI B:8Z1601 2.2 0.6 1.0
CAF B:8Z1601 2.3 0.9 1.0
CAE B:8Z1601 3.1 0.4 1.0
CAB B:8Z1601 3.1 0.2 1.0
NAU B:8Z1601 4.0 0.4 1.0
CE B:LYS409 4.0 72.5 1.0
CG B:LYS409 4.1 70.4 1.0
CAA B:8Z1601 4.4 0.7 1.0
CAD B:8Z1601 4.4 0.6 1.0
CD B:LYS409 4.5 71.4 1.0
CAT B:8Z1601 4.6 0.4 1.0
CG B:PRO421 4.8 85.8 1.0
CAC B:8Z1601 4.8 0.6 1.0
O B:LYS409 5.0 66.7 1.0

Reference:

G.S.Ducker, J.M.Ghergurovich, N.Mainolfi, V.Suri, S.K.Jeong, S.Hsin-Jung Li, A.Friedman, M.G.Manfredi, Z.Gitai, H.Kim, J.D.Rabinowitz. Human Shmt Inhibitors Reveal Defective Glycine Import As A Targetable Metabolic Vulnerability of Diffuse Large B-Cell Lymphoma. Proc. Natl. Acad. Sci. V. 114 11404 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29073064
DOI: 10.1073/PNAS.1706617114
Page generated: Tue Jul 15 08:28:44 2025

Last articles

Mg in 1SO2
Mg in 1SO5
Mg in 1SO4
Mg in 1SO3
Mg in 1SNF
Mg in 1SLH
Mg in 1SL2
Mg in 1SL5
Mg in 1SKR
Mg in 1SL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy