Receptor
PDB id Resolution Class Description Source Keywords
1rb0 1.35 Å EC: 2.7.6.3 CRYSTAL STRUCTURE OF A BINARY COMPLEX OF E. COLI HPPK WITH 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.35 ANGSTROM R ESOLUTION ESCHERICHIA COLI PYROPHOSPHOKINASE PYROPHOSPHORYL TRANSFER CATALYTIC MECHANISM FOLATE HPPK PTERIN 6-HYDROXYMETHYL-78- DIHYDROPTERIN 6-HYDROXYMETHYLPTERIN TERNARY COMPLEX BINARY COMPLEX SUBSTRATE SPECIFICITY PRODUCT RELEASE ANTIMICROBIAL AGENT DRUG DESIGN X-RAY CRYSTALLOGRAPHY TRANSFERASE
Ref.: REACTION TRAJECTORY OF PYROPHOSPHORYL TRANSFER CATALYZED BY 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE. STRUCTURE V. 12 467 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HH2 A:181;
 Valid;
 none;
 submit data
353.123 C7 H9 N5 O8 P2 c1c(n...
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: HH2; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 HH2 1 1
2 PMM 0.789474 0.968254
3 HHR 0.583333 0.765625
4 PD8 0.464286 0.895522
5 HHS 0.432836 0.734375
6 NEU 0.410959 0.753623
7 NEO 0.410959 0.753623
8 MPU 0.410959 0.753623
9 BIO 0.408451 0.686567
10 2PH 0.407895 0.828571
Similar Ligands (3D)
Ligand no: 1; Ligand: HH2; Similar ligands found: 30
No: Ligand Similarity coefficient
1 88S 0.8866
2 IM5 0.8831
3 576 0.8823
4 5R9 0.8818
5 TQT 0.8783
6 OAG 0.8776
7 35K 0.8761
8 DIH 0.8749
9 GAJ 0.8724
10 FQP 0.8715
11 7JB 0.8710
12 SAQ 0.8666
13 PW8 0.8639
14 KTV 0.8630
15 5MX 0.8619
16 D5F 0.8618
17 100 0.8618
18 LFK 0.8611
19 T21 0.8610
20 NQE 0.8607
21 EZB 0.8603
22 KTM 0.8602
23 EXP 0.8600
24 KSY 0.8594
25 87F 0.8577
26 WG8 0.8571
27 CWP 0.8571
28 5RU 0.8548
29 724 0.8544
30 5XM 0.8534
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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