Receptor
PDB id Resolution Class Description Source Keywords
5FC5 1.68 Å EC: 3.1.4.- MURINE SMPDL3A IN COMPLEX WITH PHOSPHOCHOLINE MUS MUSCULUS SMPDL3A SPHINGOMYELIN NUCLEOTIDE PHOSPHOCHOLINE HYDROLAS
Ref.: STRUCTURAL BASIS FOR NUCLEOTIDE HYDROLYSIS BY THE A SPHINGOMYELINASE-LIKE PHOSPHODIESTERASE SMPDL3A. J.BIOL.CHEM. V. 291 6376 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PC A:516;
Valid;
none;
submit data
184.151 C5 H15 N O4 P C[N+]...
GOL A:521;
A:518;
A:520;
A:522;
A:519;
A:523;
A:517;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
ZN A:502;
A:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
NAG NAG FUC A:503;
Invalid;
none;
submit data n/a n/a n/a n/a
NAG NAG A:506;
Invalid;
none;
submit data
408.404 n/a O=C(N...
FUC NAG NAG A:513;
Invalid;
none;
submit data n/a n/a n/a n/a
NAG BMA NAG MAN MAN A:511;
Invalid;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FCB 1.55 Å EC: 3.1.4.- MURINE SMPDL3A IN COMPLEX WITH AMP MUS MUSCULUS SMPDL3A SPHINGOMYELIN NUCLEOTIDE AMP HYDROLASE
Ref.: STRUCTURAL BASIS FOR NUCLEOTIDE HYDROLYSIS BY THE A SPHINGOMYELINASE-LIKE PHOSPHODIESTERASE SMPDL3A. J.BIOL.CHEM. V. 291 6376 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5FC5 - PC C5 H15 N O4 P C[N+](C)(C....
2 5FCB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 5FC6 - AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5FC5 - PC C5 H15 N O4 P C[N+](C)(C....
2 5FCB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 5FC6 - AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FC5 - PC C5 H15 N O4 P C[N+](C)(C....
2 5FCB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 5FC6 - AP2 C11 H17 N5 O9 P2 c1nc(c2c(n....
4 5KAS - PC C5 H15 N O4 P C[N+](C)(C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PC; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 PC 1 1
2 OPE 0.518519 0.680851
3 CH5 0.45 0.84
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FCB; Ligand: AMP; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 5fcb.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4J6O CIT 0.00004903 0.51695 1.89394
2 2ZO9 MLI 0.000000065 0.68381 2.07852
3 3RL3 5GP 0.000001106 0.61225 2.36486
4 2C9E DGD 0.02145 0.40213 3.36391
5 5IHE D5M 0.0000000931 0.64873 3.4642
6 4ZX2 4TE 0.0000009877 0.58076 3.6036
7 4DHL 0K7 0.000007406 0.56843 3.99061
8 4PEG 5GP 0.0000284 0.48066 4.16667
9 1HP1 ATP 0.001131 0.47112 5.08083
10 1D0L BLG 0.01252 0.43096 6.21118
11 1II7 DA 0.00000008727 0.58144 12.012
12 3IB8 AMP 0.002623 0.47342 12.1212
13 5I85 PC 0.000000000009716 0.73796 47.5751
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