Receptor
PDB id Resolution Class Description Source Keywords
1RF6 1.9 Å EC: 2.5.1.19 STRUCTURAL STUDIES OF STREPTOCOCCUS PNEUMONIAE EPSP SYNTHASE IN S3P-GLP BOUND STATE STREPTOCOCCUS PNEUMONIAE SHIKIMATE PATHWAY EPSP SYNTHASE S3P GLYPHOSATE PEP S. PNEUMONIAE TRANSFERASE
Ref.: STRUCTURAL STUDIES OF STREPTOCOCCUS PNEUMONIAE EPSP SYNTHASE IN UNLIGANDED STATE, TETRAHEDRAL INTERMEDIATE-BOUND STATE AND S3P-GLP-BOUND STATE. MOL.MICROBIOL. V. 51 963 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GPJ A:1428;
B:1528;
C:1628;
D:1728;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
170.081 C3 H9 N O5 P C(C(=...
S3P A:1429;
B:1529;
C:1629;
D:1729;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
254.131 C7 H11 O8 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RF6 1.9 Å EC: 2.5.1.19 STRUCTURAL STUDIES OF STREPTOCOCCUS PNEUMONIAE EPSP SYNTHASE IN S3P-GLP BOUND STATE STREPTOCOCCUS PNEUMONIAE SHIKIMATE PATHWAY EPSP SYNTHASE S3P GLYPHOSATE PEP S. PNEUMONIAE TRANSFERASE
Ref.: STRUCTURAL STUDIES OF STREPTOCOCCUS PNEUMONIAE EPSP SYNTHASE IN UNLIGANDED STATE, TETRAHEDRAL INTERMEDIATE-BOUND STATE AND S3P-GLP-BOUND STATE. MOL.MICROBIOL. V. 51 963 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1RF6 - S3P C7 H11 O8 P C1[C@H]([C....
2 1RF4 - SPQ C10 H15 F O14 P2 C1[C@H]([C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1RF6 - S3P C7 H11 O8 P C1[C@H]([C....
2 1RF4 - SPQ C10 H15 F O14 P2 C1[C@H]([C....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2GGA Ki = 6 mM GPJ C3 H9 N O5 P C(C(=O)O)[....
2 2GGD ic50 = 160 uM GPJ C3 H9 N O5 P C(C(=O)O)[....
3 2PQB Ki = 63 nM GG9 C10 H14 F2 O14 P2 C1[C@H]([C....
4 2GG6 - S3P C7 H11 O8 P C1[C@H]([C....
5 2PQC Ki = 1800 nM RC1 C10 H16 O13 P2 C[C@@](C(=....
6 2PQD - GG9 C10 H14 F2 O14 P2 C1[C@H]([C....
7 1RF6 - S3P C7 H11 O8 P C1[C@H]([C....
8 1RF4 - SPQ C10 H15 F O14 P2 C1[C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GPJ; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 GPJ 1 1
2 PAE 0.423077 0.625
Ligand no: 2; Ligand: S3P; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 S3P 1 1
2 EPS 0.545455 0.897436
3 RC1 0.508475 0.875
4 SC1 0.508475 0.875
5 SKP 0.491803 0.897436
6 SPQ 0.46875 0.813953
7 GG9 0.461538 0.875
8 SKM 0.456522 0.641026
9 6TO 0.421875 0.675
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RF6; Ligand: GPJ; Similar sites found: 16
This union binding pocket(no: 1) in the query (biounit: 1rf6.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U4L H1S 0.02402 0.4136 None
2 5AHO TLA 0.02967 0.40682 2.38095
3 4RF7 ARG 0.01663 0.41332 2.57611
4 5X7Q GLC GLC GLC 0.002724 0.46786 3.27869
5 5X7Q GLC GLC GLC GLC 0.00281 0.4664 3.27869
6 3ACC 5GP 0.009546 0.42249 3.31492
7 4HGD KGT 0.0113 0.40665 3.51906
8 2JBH 5GP 0.02606 0.40041 3.55556
9 4BG4 ARG 0.009905 0.42978 3.65169
10 4WGF HX2 0.01162 0.4227 5.36585
11 2YN4 39J 0.03186 0.40007 6.35593
12 2BZ1 TAU 0.01124 0.43538 6.63265
13 1TUU ADP 0.02602 0.40455 7.01754
14 1K4M CIT 0.0212 0.4209 8.4507
15 3N6M GTP 0.02193 0.40422 17.3302
16 3ZH4 FLC 0.01065 0.40142 36.5155
Pocket No.: 2; Query (leader) PDB : 1RF6; Ligand: S3P; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 1rf6.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U4L H1S 0.02402 0.4136 None
2 5AHO TLA 0.02967 0.40682 2.38095
3 4RF7 ARG 0.01663 0.41332 2.57611
4 3JU6 ARG 0.02301 0.40993 3.24324
5 5X7Q GLC GLC GLC 0.002724 0.46786 3.27869
6 5X7Q GLC GLC GLC GLC 0.00281 0.4664 3.27869
7 4HGD KGT 0.0113 0.40665 3.51906
8 4BG4 ARG 0.009905 0.42978 3.65169
9 4WGF HX2 0.01162 0.4227 5.36585
10 2YN4 39J 0.03186 0.40007 6.35593
11 1TUU ADP 0.02602 0.40455 7.01754
12 1K4M CIT 0.0212 0.4209 8.4507
13 3N6M GTP 0.02193 0.40422 17.3302
14 3ZH4 FLC 0.01065 0.40142 36.5155
Pocket No.: 3; Query (leader) PDB : 1RF6; Ligand: GPJ; Similar sites found: 8
This union binding pocket(no: 3) in the query (biounit: 1rf6.bio3) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FJJ MAN 0.008443 0.44339 1.87354
2 1QH8 HCA 0.03252 0.40017 2.57611
3 4BHL ARG 0.02456 0.40179 3.65169
4 1GXS BEZ 0.03366 0.40226 3.79747
5 2AF6 BRU 0.02244 0.41227 4.65116
6 3W9F I3P 0.01151 0.42733 7.69231
7 1MAI I3P 0.02456 0.41132 11.4504
8 3VCY UD1 0.005285 0.40277 43.0913
Pocket No.: 4; Query (leader) PDB : 1RF6; Ligand: S3P; Similar sites found: 14
This union binding pocket(no: 4) in the query (biounit: 1rf6.bio3) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FJJ MAN 0.008895 0.44339 1.87354
2 5FYR INS 0.02468 0.40443 2.34899
3 1QH8 HCA 0.03436 0.40017 2.57611
4 3ACC 5GP 0.008464 0.42829 3.31492
5 2JBH 5GP 0.02308 0.40606 3.55556
6 4BHL ARG 0.02599 0.40179 3.65169
7 1GXS BEZ 0.03575 0.40226 3.79747
8 2AF6 BRU 0.02144 0.41469 4.65116
9 3HAV ATP 0.01849 0.41753 6.02007
10 2BZ1 TAU 0.01385 0.42977 6.63265
11 3W9F I3P 0.01217 0.42733 7.69231
12 1DCP HBI 0.02292 0.4034 8.65385
13 1MAI I3P 0.02058 0.41569 11.4504
14 3VCY UD1 0.005773 0.40277 43.0913
Pocket No.: 5; Query (leader) PDB : 1RF6; Ligand: S3P; Similar sites found: 2
This union binding pocket(no: 5) in the query (biounit: 1rf6.bio4) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AHS SIN 0.03134 0.40513 4.48878
2 1LT3 GAL BGC 0.01867 0.40692 10.6796
Pocket No.: 6; Query (leader) PDB : 1RF6; Ligand: GPJ; Similar sites found: 3
This union binding pocket(no: 6) in the query (biounit: 1rf6.bio4) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FYR INS 0.02092 0.40503 2.34899
2 5AHS SIN 0.03134 0.40513 4.48878
3 1LT3 GAL BGC 0.01867 0.40692 10.6796
Pocket No.: 7; Query (leader) PDB : 1RF6; Ligand: GPJ; Similar sites found: 3
This union binding pocket(no: 7) in the query (biounit: 1rf6.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GCG DGY 0.04283 0.40116 2.12121
2 1IGW PYR 0.0326 0.40133 3.27869
3 1P0Z FLC 0.0293 0.40336 6.87023
Pocket No.: 8; Query (leader) PDB : 1RF6; Ligand: S3P; Similar sites found: 3
This union binding pocket(no: 8) in the query (biounit: 1rf6.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GCG DGY 0.04283 0.40116 2.12121
2 1IGW PYR 0.0326 0.40133 3.27869
3 1P0Z FLC 0.0293 0.40336 6.87023
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