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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

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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

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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

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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

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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

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