Atomistry » Fluorine » PDB 5uv2-5vd2 » 5v7i
Atomistry »
  Fluorine »
    PDB 5uv2-5vd2 »
      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: Thu Aug 1 15:58:13 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy