Receptor
PDB id Resolution Class Description Source Keywords
5FEX 1.32 Å EC: 7.-.-.- HYDE FROM T. MARITIMA IN COMPLEX WITH SE-ADENOSYL-L-SELENOCY (TFINAL OF THE REACTION) THERMOTOGA MARITIMA RADICAL SAM ENZYME COMPLEX FEFE-HYDROGENASE MATURASE THAZOXIDOREDUCTASE
Ref.: CARBON-SULFUR BOND-FORMING REACTION CATALYSED BY TH SAM ENZYME HYDE. NAT.CHEM. V. 8 491 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CPS A:404;
A:405;
A:406;
A:403;
A:402;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
614.877 C32 H58 N2 O7 S C[C@H...
CL A:409;
A:408;
A:407;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
5AD SEC A:410;
Valid;
none;
submit data n/a n/a n/a n/a
SF4 A:401;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
MET A:411;
Valid;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JYD 1.71 Å EC: 7.-.-.- X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TIME COURSE SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 CLUSTERS. THERMOTOGA MARITIMA RADICAL SAM PROTEIN FEFE-HYDROGENASE ACTIVE SITE ASSEMBLY CLUSTER S-ADENOSYL-L-METHIONINE OXIDOREDUCTASE
Ref.: X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TI OF SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 CLUSTERS. PROC.NATL.ACAD.SCI.USA V. 110 7188 2013
Members (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 3CIW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JYE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 3CIX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5FEX - 5AD SEC n/a n/a
5 5FF3 - PRS C4 H7 N O2 S C1[C@H](NC....
6 5FEP - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 3IIZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 5FES - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 5FF0 - 5X8 C13 H18 N6 O5 S c1nc(c2c(n....
10 4JXC - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 4JY9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4JYF - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5FF4 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
14 3IIX - MET C5 H11 N O2 S CSCC[C@@H]....
15 4JYD - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5FEW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5FF2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
18 5FEZ - 9SE C6 H9 N O4 Se C[C@]1(N[C....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3CIW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JYE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 3CIX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5FEX - 5AD SEC n/a n/a
5 5FF3 - PRS C4 H7 N O2 S C1[C@H](NC....
6 5FEP - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 3IIZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 5FES - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 5FF0 - 5X8 C13 H18 N6 O5 S c1nc(c2c(n....
10 4JXC - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 4JY9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4JYF - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5FF4 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
14 3IIX - MET C5 H11 N O2 S CSCC[C@@H]....
15 4JYD - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5FEW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5FF2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
18 5FEZ - 9SE C6 H9 N O4 Se C[C@]1(N[C....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3CIW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4JYE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 3CIX - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 5FEX - 5AD SEC n/a n/a
5 5FF3 - PRS C4 H7 N O2 S C1[C@H](NC....
6 5FEP - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 3IIZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
8 5FES - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 5FF0 - 5X8 C13 H18 N6 O5 S c1nc(c2c(n....
10 4JXC - SAM C15 H22 N6 O5 S C[S@@+](CC....
11 4JY9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4JYF - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5FF4 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
14 3IIX - MET C5 H11 N O2 S CSCC[C@@H]....
15 4JYD - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5FEW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5FF2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
18 5FEZ - 9SE C6 H9 N O4 Se C[C@]1(N[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5AD SEC; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Ligand no: 2; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MED 1 1
2 MET 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 MF3 0.5 0.647059
7 NVA 0.5 0.758621
8 HSE 0.466667 0.617647
9 DAB 0.466667 0.636364
10 MHO 0.457143 0.717949
11 SME 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 DGL 0.424242 0.625
22 GGL 0.424242 0.625
23 GLU 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 FME 0.410256 0.84375
27 AME 0.410256 0.771429
28 LEU 0.40625 0.666667
29 JM6 0.4 0.7
30 CYS 0.4 0.666667
31 DCY 0.4 0.666667
32 C2N 0.4 0.633333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JYD; Ligand: SAH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4jyd.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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