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Receptor
PDB id Resolution Class Description Source Keywords
1KYV 2.4 Å EC: 2.5.1.9 LUMAZINE SYNTHASE FROM S.POMBE BOUND TO RIBOFLAVIN SCHIZOSACCHAROMYCES POMBE RIBOFLAVIN BIOSYNTHESIS LUMAZINE SYNTHASE SCHIZOSACCHAROMYPOMBE LIGAND BINDING TRANSFERASE
Ref.: THE STRUCTURAL BASIS OF RIBOFLAVIN BINDING TO SCHIZOSACCHAROMYCES POMBE 6,7-DIMETHYL-8-RIBITYLLUM SYNTHASE. J.MOL.BIOL. V. 318 1317 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:1004;
B:1001;
C:1003;
D:1005;
E:1002;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
RBF A:501;
B:502;
C:503;
D:504;
E:505;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Kd = 1.2 uM
376.364 C17 H20 N4 O6 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KYV 2.4 Å EC: 2.5.1.9 LUMAZINE SYNTHASE FROM S.POMBE BOUND TO RIBOFLAVIN SCHIZOSACCHAROMYCES POMBE RIBOFLAVIN BIOSYNTHESIS LUMAZINE SYNTHASE SCHIZOSACCHAROMYPOMBE LIGAND BINDING TRANSFERASE
Ref.: THE STRUCTURAL BASIS OF RIBOFLAVIN BINDING TO SCHIZOSACCHAROMYCES POMBE 6,7-DIMETHYL-8-RIBITYLLUM SYNTHASE. J.MOL.BIOL. V. 318 1317 2002
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1KYV Kd = 1.2 uM RBF C17 H20 N4 O6 Cc1cc2c(cc....
2 1KYY - INI C9 H14 N4 O8 C([C@@H]([....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1KYV Kd = 1.2 uM RBF C17 H20 N4 O6 Cc1cc2c(cc....
2 1KYY - INI C9 H14 N4 O8 C([C@@H]([....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4KQ6 - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 2C97 Ka = 1380000 M^-1 JCL C8 H12 Cl N2 O6 P C(CCOP(=O)....
3 2C94 Ka = 6540000 M^-1 TSF C15 H23 F2 N4 O10 P C(CCN1C2=C....
4 1W19 - T1P C13 H21 N4 O11 P C(CN1C2=C(....
5 2C92 Ka = 4500 M^-1 TP6 C15 H25 N4 O11 P C(CCN1C2=C....
6 2VI5 Ki = 110 uM Y19 C12 H20 N4 O7 CCC(=O)N[C....
7 1W29 - TS0 C14 H23 N4 O11 P C(CCOP(=O)....
8 1NQX - RLP C14 H18 N4 O9 C(CC(=O)O)....
9 1NQU - RDL C11 H14 N4 O8 C([C@@H]([....
10 1NQW - 5YL C14 H26 N3 O9 P C(CCC1=C(N....
11 1NQV - LMZ C9 H14 N4 O7 C([C@@H]([....
12 1RVV - INI C9 H14 N4 O8 C([C@@H]([....
13 1KYV Kd = 1.2 uM RBF C17 H20 N4 O6 Cc1cc2c(cc....
14 1KYY - INI C9 H14 N4 O8 C([C@@H]([....
15 1EJB - INJ C14 H26 N3 O9 P C(CCc1c(nc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RBF; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 RBF 1 1
2 FMN 0.75641 0.876712
3 RS3 0.74026 0.942029
4 DLZ 0.546667 0.885714
5 1VY 0.525641 0.871429
6 C3F 0.523256 0.816901
7 LFN 0.513889 0.712121
8 CF4 0.511364 0.805556
9 FAD 0.460938 0.790123
10 FAS 0.460938 0.790123
11 FAE 0.457364 0.780488
12 RLP 0.438202 0.833333
13 FO1 0.423913 0.871429
14 HDF 0.423913 0.871429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: 40
This union binding pocket(no: 1) in the query (biounit: 1kyv.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5CMK GLU None
2 3OEN GLU 1.25786
3 3BJE URA 1.25786
4 4K7O EKZ 3.14465
5 4YRY NAD 3.14465
6 4YRY FAD 3.14465
7 5NM7 GLY 3.77358
8 1KQR MNA 4.40252
9 3OG9 MLT 4.40252
10 2JK0 ASP 4.40252
11 4DYG MES 4.40252
12 4UBS DIF 4.40252
13 1QH8 HCA 5.03145
14 1KC7 PPR 5.03145
15 2VWT PYR 5.66038
16 3CV2 OXL 6.28931
17 4WES HCA 6.91824
18 1D8C GLV 6.91824
19 2RC8 DSN 6.91824
20 3FV1 DYH 7.54717
21 1P7T PYR 7.54717
22 3KVY URA 8.1761
23 4D7E FAD 8.1761
24 5W8Q BU4 8.1761
25 1UGY GLA GLC 8.27068
26 2B6N ALA PRO THR 8.27338
27 2WPB ZZI 8.80503
28 5BSH PRO 8.80503
29 6C0B MLI 8.97436
30 1M5B BN1 9.43396
31 4F2Q QUS 9.43396
32 2NU5 NAG 9.83607
33 2NUO BGC 9.83607
34 3U7Q HCA 10.0629
35 4DS0 A2G GAL NAG FUC 10.6918
36 3BMN AX3 13.8365
37 3JUC PCA 14.3791
38 3GCM 5GP 15.0943
39 5KOH HCA 21.3836
40 2XZ9 PYR 22.0126
Pocket No.: 2; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1kyv.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 1kyv.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2R5N RP5 3.77358
2 2R5N TPP 3.77358
3 1Q19 SSC 4.40252
4 5O4F 8VE 6.91824
5 3ALT MLB 7.64331
6 3NFD COA 12.4183
Pocket No.: 4; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1kyv.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: 2
This union binding pocket(no: 5) in the query (biounit: 1kyv.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2RCA GLY 3.77358
2 1SNN 5RP 7.54717
Pocket No.: 6; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1kyv.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: 6
This union binding pocket(no: 7) in the query (biounit: 1kyv.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3BD9 A3P 1.88679
2 1NAA ABL 3.77358
3 4YNU LGC 5.03145
4 4YNU FAD 5.03145
5 1JG3 ADN 5.66038
6 3W9F I3P 6.28931
Pocket No.: 8; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1kyv.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: 5
This union binding pocket(no: 9) in the query (biounit: 1kyv.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1M7Y PPG 4.40252
2 1EI6 PPF 5.03145
3 3Q9T FAY 7.54717
4 1MZC BNE 11.9497
5 1MZC FPP 11.9497
Pocket No.: 10; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 1kyv.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 1kyv.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 1kyv.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 1kyv.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 1kyv.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 1KYV; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 15) in the query (biounit: 1kyv.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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