Receptor
PDB id Resolution Class Description Source Keywords
4F7V 1.73 Å EC: 2.7.6.3 CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRAT INHIBITOR J1D (HP26) ESCHERICHIA COLI ALPHA BETA PYROPHOSPHOKINASE PYROPHOSPHORYL TRANSFER TRANTRANSFERASE INHIBITOR COMPLEX
Ref.: BISUBSTRATE ANALOG INHIBITORS OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE LEAD EXHIBITS A DISTINCT BINDING MODE. BIOORG.MED.CHEM. V. 20 4303 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
J1D A:201;
 Valid;
 none;
 Kd = 4.16 uM
634.625 C23 H30 N12 O8 S CC1(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
7KDR 1.49 Å EC: 2.7.6.3 CRYSTAL STRUCTURE OF ESCHERICHIA COLI HPPK IN COMPLEX WITH B INHIBITOR HP-75 ESCHERICHIA COLI (STRAIN K12) ALPHA BETA TRANSFERASE TRANSFERASE-INHIBITOR COMPLEX
Ref.: BISUBSTRATE INHIBITORS OF 6-HYDROXYMETHYL-7,8-DIHYD PYROPHOSPHOKINASE: TRANSITION STATE ANALOGS FOR HIG AFFINITY BINDING. BIOORG.MED.CHEM. 15847 2020
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3HD1 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
2 5ETO Kd = 2.7 uM 5RY C13 H9 F N6 O S c1cc(c(cc1....
3 1HQ2 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
4 3HT0 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
5 4M5J Kd = 14.5 uM YH5 C14 H13 N5 O3 S COc1ccc(cc....
6 5ETP Kd = 0.7 uM 5RZ C13 H10 Br N5 O2 S c1cc(ccc1C....
7 1DY3 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 5ETM Kd = 3.9 uM 5RW C12 H10 F N5 O S c1cc(ccc1C....
9 3HSG - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
10 5ETN Kd = 4.3 uM 5RX C12 H10 Cl N5 O S c1cc(ccc1C....
11 4M5M Kd = 18 uM DX4 C5 H5 N5 S c1[nH]c2c(....
12 1EX8 Kd = 0.47 uM A4P C17 H24 N10 O17 P4 c1nc(c2c(n....
13 4M5H Kd = 29 uM YH2 C13 H10 N6 O S c1cc(ccc1C....
14 1EQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 3UDE - J1B C26 H38 N12 O4 S CC1(C(=NC2....
16 1Q0N - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
17 1RU2 Kd = 0.32 uM APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 3UD5 - J1A C24 H32 N12 O4 S c1c(nc2c(n....
19 4M5K Kd = 5.9 uM YH3 C14 H13 N5 O2 S Cc1cccc(c1....
20 4M5G Kd = 9.7 uM YH1 C13 H11 N5 O2 S c1ccc(cc1)....
21 5ETK Kd = 1.5 uM 5RU C12 H10 F N5 O S c1ccc(c(c1....
22 3IP0 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
23 3ILO - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
24 3HD2 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
25 4M5N Kd = 7.5 uM YH7 C5 H5 N5 S C1=NC2=C(N....
26 1RB0 - HH2 C7 H9 N5 O8 P2 c1c(nc2c(n....
27 5ETL Kd = 23 uM 5RV C13 H10 N6 O S c1ccc(c(c1....
28 4M5I Kd = 6.7 uM YH6 C14 H13 N5 O2 S Cc1ccc(cc1....
29 4F7V Kd = 4.16 uM J1D C23 H30 N12 O8 S CC1(C(=NC2....
30 1RU1 Kd = 18 uM PH2 C7 H9 N5 O2 C1C(=NC2=C....
31 3KUH - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
32 7KDR Kd = 0.047 uM J1L C27 H36 N12 O9 S CC1(C(=NC2....
33 1F9H - PH2 C7 H9 N5 O2 C1C(=NC2=C....
34 3UDV Kd = 2.55 uM J1C C26 H36 N12 O5 S CC1(C(=NC2....
35 1RAO - HH2 C7 H9 N5 O8 P2 c1c(nc2c(n....
36 7KDO ic50 = 0.38 uM H73 C27 H36 N12 O7 S CC1(C(=NC2....
37 1TMM Kd = 0.23 uM APC C11 H18 N5 O12 P3 c1nc(c2c(n....
38 4M5L Kd = 18.9 uM YH4 C14 H13 N5 O2 S Cc1ccccc1C....
70% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3HD1 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
2 5ETO Kd = 2.7 uM 5RY C13 H9 F N6 O S c1cc(c(cc1....
3 1HQ2 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
4 3HT0 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
5 4M5J Kd = 14.5 uM YH5 C14 H13 N5 O3 S COc1ccc(cc....
6 5ETP Kd = 0.7 uM 5RZ C13 H10 Br N5 O2 S c1cc(ccc1C....
7 1DY3 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 5ETM Kd = 3.9 uM 5RW C12 H10 F N5 O S c1cc(ccc1C....
9 3HSG - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
10 5ETN Kd = 4.3 uM 5RX C12 H10 Cl N5 O S c1cc(ccc1C....
11 4M5M Kd = 18 uM DX4 C5 H5 N5 S c1[nH]c2c(....
12 1EX8 Kd = 0.47 uM A4P C17 H24 N10 O17 P4 c1nc(c2c(n....
13 4M5H Kd = 29 uM YH2 C13 H10 N6 O S c1cc(ccc1C....
14 1EQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 3UDE - J1B C26 H38 N12 O4 S CC1(C(=NC2....
16 1Q0N - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
17 1RU2 Kd = 0.32 uM APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 3UD5 - J1A C24 H32 N12 O4 S c1c(nc2c(n....
19 4M5K Kd = 5.9 uM YH3 C14 H13 N5 O2 S Cc1cccc(c1....
20 4M5G Kd = 9.7 uM YH1 C13 H11 N5 O2 S c1ccc(cc1)....
21 5ETK Kd = 1.5 uM 5RU C12 H10 F N5 O S c1ccc(c(c1....
22 3IP0 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
23 3ILO - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
24 3HD2 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
25 4M5N Kd = 7.5 uM YH7 C5 H5 N5 S C1=NC2=C(N....
26 1RB0 - HH2 C7 H9 N5 O8 P2 c1c(nc2c(n....
27 5ETL Kd = 23 uM 5RV C13 H10 N6 O S c1ccc(c(c1....
28 4M5I Kd = 6.7 uM YH6 C14 H13 N5 O2 S Cc1ccc(cc1....
29 4F7V Kd = 4.16 uM J1D C23 H30 N12 O8 S CC1(C(=NC2....
30 1RU1 Kd = 18 uM PH2 C7 H9 N5 O2 C1C(=NC2=C....
31 3KUH - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
32 7KDR Kd = 0.047 uM J1L C27 H36 N12 O9 S CC1(C(=NC2....
33 1F9H - PH2 C7 H9 N5 O2 C1C(=NC2=C....
34 3UDV Kd = 2.55 uM J1C C26 H36 N12 O5 S CC1(C(=NC2....
35 1RAO - HH2 C7 H9 N5 O8 P2 c1c(nc2c(n....
36 7KDO ic50 = 0.38 uM H73 C27 H36 N12 O7 S CC1(C(=NC2....
37 1TMM Kd = 0.23 uM APC C11 H18 N5 O12 P3 c1nc(c2c(n....
38 4M5L Kd = 18.9 uM YH4 C14 H13 N5 O2 S Cc1ccccc1C....
39 2QX0 Kd = 0.78 uM PH2 C7 H9 N5 O2 C1C(=NC2=C....
40 1CBK - ROI C8 H11 N5 O2 CC1(C(=NC2....
50% Homology Family (49)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3HD1 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
2 5ETO Kd = 2.7 uM 5RY C13 H9 F N6 O S c1cc(c(cc1....
3 1HQ2 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
4 3HT0 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
5 4M5J Kd = 14.5 uM YH5 C14 H13 N5 O3 S COc1ccc(cc....
6 5ETP Kd = 0.7 uM 5RZ C13 H10 Br N5 O2 S c1cc(ccc1C....
7 1DY3 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 5ETM Kd = 3.9 uM 5RW C12 H10 F N5 O S c1cc(ccc1C....
9 3HSG - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
10 5ETN Kd = 4.3 uM 5RX C12 H10 Cl N5 O S c1cc(ccc1C....
11 4M5M Kd = 18 uM DX4 C5 H5 N5 S c1[nH]c2c(....
12 1EX8 Kd = 0.47 uM A4P C17 H24 N10 O17 P4 c1nc(c2c(n....
13 4M5H Kd = 29 uM YH2 C13 H10 N6 O S c1cc(ccc1C....
14 1EQM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 3UDE - J1B C26 H38 N12 O4 S CC1(C(=NC2....
16 1Q0N - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
17 1RU2 Kd = 0.32 uM APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 3UD5 - J1A C24 H32 N12 O4 S c1c(nc2c(n....
19 4M5K Kd = 5.9 uM YH3 C14 H13 N5 O2 S Cc1cccc(c1....
20 4M5G Kd = 9.7 uM YH1 C13 H11 N5 O2 S c1ccc(cc1)....
21 5ETK Kd = 1.5 uM 5RU C12 H10 F N5 O S c1ccc(c(c1....
22 3IP0 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
23 3ILO - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
24 3HD2 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
25 4M5N Kd = 7.5 uM YH7 C5 H5 N5 S C1=NC2=C(N....
26 1RB0 - HH2 C7 H9 N5 O8 P2 c1c(nc2c(n....
27 5ETL Kd = 23 uM 5RV C13 H10 N6 O S c1ccc(c(c1....
28 4M5I Kd = 6.7 uM YH6 C14 H13 N5 O2 S Cc1ccc(cc1....
29 4F7V Kd = 4.16 uM J1D C23 H30 N12 O8 S CC1(C(=NC2....
30 1RU1 Kd = 18 uM PH2 C7 H9 N5 O2 C1C(=NC2=C....
31 3KUH - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
32 7KDR Kd = 0.047 uM J1L C27 H36 N12 O9 S CC1(C(=NC2....
33 1F9H - PH2 C7 H9 N5 O2 C1C(=NC2=C....
34 3UDV Kd = 2.55 uM J1C C26 H36 N12 O5 S CC1(C(=NC2....
35 1RAO - HH2 C7 H9 N5 O8 P2 c1c(nc2c(n....
36 7KDO ic50 = 0.38 uM H73 C27 H36 N12 O7 S CC1(C(=NC2....
37 1TMM Kd = 0.23 uM APC C11 H18 N5 O12 P3 c1nc(c2c(n....
38 4M5L Kd = 18.9 uM YH4 C14 H13 N5 O2 S Cc1ccccc1C....
39 2QX0 Kd = 0.78 uM PH2 C7 H9 N5 O2 C1C(=NC2=C....
40 1CBK - ROI C8 H11 N5 O2 CC1(C(=NC2....
41 4AD6 Kd = 16.7 uM GSY C7 H9 N5 O2 S C(CO)n1c2c....
42 5ETQ Kd = 0.33 uM YH2 C13 H10 N6 O S c1cc(ccc1C....
43 5ETR Kd = 0.3 uM 5RW C12 H10 F N5 O S c1cc(ccc1C....
44 4CRJ Kd = 1.1 uM YH5 C14 H13 N5 O3 S COc1ccc(cc....
45 4CWB Kd = 0.81 uM X6L C19 H15 N5 O2 S c1ccc(cc1)....
46 5ETS Kd = 1.24 uM 5RX C12 H10 Cl N5 O S c1cc(ccc1C....
47 3QBC Kd = 10.8 uM B55 C5 H5 N5 O S c12c([nH]c....
48 5ETT Kd = 0.59 uM 5RY C13 H9 F N6 O S c1cc(c(cc1....
49 5ETV Kd = 0.57 uM 5RZ C13 H10 Br N5 O2 S c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: J1D; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 J1D 1 1
2 J1L 0.617647 0.959596
3 J1C 0.588235 0.877551
4 H73 0.559441 0.868687
5 J1B 0.458904 0.858586
6 RAB 0.415094 0.625
7 ADN 0.415094 0.625
8 XYA 0.415094 0.625
9 MTA 0.410714 0.628866
10 A4P 0.408451 0.78
11 5N5 0.407407 0.642105
12 GJV 0.40678 0.701031
13 TSB 0.40625 0.708738
14 6RE 0.405172 0.708333
15 MHZ 0.404959 0.660194
16 G5A 0.403226 0.728155
Similar Ligands (3D)
Ligand no: 1; Ligand: J1D; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 7KDR; Ligand: J1L; 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: 7kdr.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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