Receptor
PDB id Resolution Class Description Source Keywords
4mcc 1.95 Å EC: 2.1.1.228 HINTRMD IN COMPLEX WITH N-[4-(AMINOMETHYL)BENZYL]-4-OXO-3,4- DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE HAEMOPHILUS INFLUENZAE TREFOIL TRMD SAM SAH SINEFUNGIN HMT STRUCTURAL GENOMICTRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: SELECTIVE INHIBITORS OF BACTERIAL T-RNA-(N(1)G37) METHYLTRANSFERASE (TRMD) THAT DEMONSTRATE NOVEL ORD THE LID DOMAIN. J.MED.CHEM. V. 56 7278 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
21X B:301;
A:301;
 Valid;
Valid;
 none;
none;
 ic50 = 0.56 uM
314.362 C15 H14 N4 O2 S c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MCC 1.95 Å EC: 2.1.1.228 HINTRMD IN COMPLEX WITH N-[4-(AMINOMETHYL)BENZYL]-4-OXO-3,4- DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE HAEMOPHILUS INFLUENZAE TREFOIL TRMD SAM SAH SINEFUNGIN HMT STRUCTURAL GENOMICTRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: SELECTIVE INHIBITORS OF BACTERIAL T-RNA-(N(1)G37) METHYLTRANSFERASE (TRMD) THAT DEMONSTRATE NOVEL ORD THE LID DOMAIN. J.MED.CHEM. V. 56 7278 2013
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
2 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
3 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
4 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
6 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
9 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6JOE Kd = 0.091 uM BWR C20 H23 N5 O2 S c1cc(ccc1C....
2 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
3 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
4 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
5 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
6 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
11 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6QQR - JDN C8 H8 B N O2 B(c1ccc2c(....
2 6QOA - JBN C4 H4 N2 O2 c1cnoc1C(=....
3 6QOF - ADE C5 H5 N5 c1[nH]c2c(....
4 6QQY Kd = 0.5 uM JD2 C18 H14 N6 c1ccnc(c1)....
5 6QRF Kd = 33 uM JF5 C11 H10 N2 O2 c1ccc(cc1)....
6 6QOJ - JBH C8 H8 N2 O c1ccc2c(c1....
7 6QR5 Kd = 0.49 uM JFH C23 H25 N5 c1cc(ccc1C....
8 6QOR - JBK C6 H6 N2 O3 c1cc(c(c(c....
9 6QON - J9W C8 H5 N O3 c1ccc2c(c1....
10 6QOO - JAB C4 H4 N2 O S c1cnoc1C(=....
11 6QOK - J9T C7 H8 N2 O2 COC(=O)c1c....
12 6QR6 Kd = 0.027 uM JCK C24 H24 N6 c1cc(ccc1C....
13 6QQS Kd = 110 uM JCZ C11 H10 N4 c1cc(cc2c1....
14 6QQZ Kd = 0.18 uM JEB C18 H14 N6 c1cc(cnc1)....
15 6QO4 - 97T C9 H7 N O2 c1ccc(c(c1....
16 6QQW Kd = 19 uM JDQ C18 H16 N4 c1ccc(cc1)....
17 6QQT Kd = 59 uM JCH C19 H18 N4 O COc1ccc(cc....
18 6QQQ Kd = 6.7 uM JDE C17 H15 N3 O3 COc1cc(cc(....
19 6QOC - J9Q C9 H8 N2 O c1ccc(c(c1....
20 6NW6 - SAM C15 H22 N6 O5 S C[S@@+](CC....
21 6QO3 - J9N C7 H7 N3 S c1cc(sc1)C....
22 6QR7 Kd = 70 nM JEK C25 H26 N6 c1cc(ccc1C....
23 6QOT Kd = 0.17 mM 6SD C10 H11 N3 O COc1ccc(cc....
24 6QR0 Kd = 0.12 uM JFB C18 H14 N6 c1cc(cc2c1....
25 6QR9 Kd = 190 nM JEE C24 H24 N6 O c1cc(ccc1C....
26 6QOQ - JAE C7 H6 N2 S c1cc2c(cc1....
27 6QOD - FBB C7 H5 F N2 S c1cc2c(cc1....
28 6QOV - JAH C12 H12 N2 c1ccc(cc1)....
29 6QR1 Kd = 8.5 uM JFT C18 H13 Cl N6 c1cc(cnc1)....
30 6QOI - ABV C7 H6 N2 S c1ccc2c(c1....
31 6QRC Kd = 13 uM JFE C19 H18 N4 O COc1cccc(c....
32 6QOW - JBZ C9 H7 N O3 S COc1ccc2c(....
33 6QRE Kd = 14 uM JCQ C12 H12 N2 O3 COc1cccc(c....
34 6QOX - JA5 C9 H9 N O3 S COC(=O)c1c....
35 6QOG - JA8 C7 H5 Br N2 S c1cc2c(cc1....
36 6QR2 Kd = 3.2 uM JQB C18 H14 N6 O c1cc(c(nc1....
37 6QQV Kd = 12 uM JEW C19 H15 N5 c1ccc(c(c1....
38 6NW7 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
39 6QRA Kd = 710 nM JDK C24 H27 N5 c1cc(ccc1C....
40 6QOS - GOJ C6 H8 N2 O2 CCOC(=O)c1....
41 6QRB Kd = 27 nM JEQ C25 H26 N6 c1ccc(cc1)....
42 6QR8 Kd = 0.073 uM JDH C25 H27 N7 CN1CCN(CC1....
43 6QO6 - 5OB C8 H8 N2 O COc1ccc2c(....
44 6QRD Kd = 100 nM JEH C27 H31 N7 CC(C)N1CCN....
45 6QOH - 6GU C5 H4 Cl N5 c1[nH]c2c(....
46 6QOP - JBQ C8 H7 F N2 O c1cc2c(c(c....
47 6QR3 Kd = 0.36 uM JE8 C19 H22 N6 CN1CCC[C@@....
48 6QOL - JB5 C8 H7 N3 c1cc2c(cc1....
49 6QQU Kd = 5 uM JF8 C12 H9 N5 c1cc(cc2c1....
50 6QOM - JBE C5 H5 N3 O2 c1cc(c(nc1....
51 6QRG Kd = 10 uM JET C14 H14 N2 O5 COC(=O)COc....
52 6QR4 Kd = 0.59 uM JD8 C19 H22 N6 CN1CCCC[C@....
53 6QO2 - JAW C9 H8 N2 O c1cc2c(cc[....
54 6QOU Kd = 0.26 mM JB8 C8 H8 B N O2 B(c1ccc2cc....
55 6JOE Kd = 0.091 uM BWR C20 H23 N5 O2 S c1cc(ccc1C....
56 4MCD ic50 = 4.7 uM 22L C12 H8 N2 O S c1ccc(cc1)....
57 3AXZ Kd = 372 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
58 4MCC ic50 = 0.56 uM 21X C15 H14 N4 O2 S c1cc(ccc1C....
59 1UAK - SAM C15 H22 N6 O5 S C[S@@+](CC....
60 4YVH - SFG C15 H23 N7 O5 c1nc(c2c(n....
61 1UAL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
62 1UAM - SAH C14 H20 N6 O5 S c1nc(c2c(n....
63 4YVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
64 4MCB ic50 = 1.5 uM 21W C19 H18 N6 O2 S c1cc(ccc1C....
65 5ZHJ Kd = 10.1 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
66 5ZHL Kd = 0.19 uM 9D0 C23 H30 N4 O2 S CCCCCCCCNC....
67 5ZHK - 9D6 C23 H28 N4 O2 S CCN(Cc1ccc....
68 6JOF Kd = 10.4 uM BWR C20 H23 N5 O2 S c1cc(ccc1C....
69 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 21X; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 21X 1 1
2 21W 0.679487 0.836364
3 BWR 0.666667 0.783333
4 9D0 0.6625 0.754098
5 9D6 0.616279 0.754098
Similar Ligands (3D)
Ligand no: 1; Ligand: 21X; Similar ligands found: 38
No: Ligand Similarity coefficient
1 BFS 0.9097
2 4KN 0.9032
3 CHJ 0.8990
4 M62 0.8946
5 28C 0.8914
6 EUB 0.8907
7 J71 0.8869
8 PT1 0.8869
9 9RK 0.8857
10 5V3 0.8849
11 F91 0.8846
12 GKW 0.8793
13 TCW 0.8788
14 YH5 0.8782
15 WDU 0.8781
16 6EO 0.8774
17 2ZT 0.8771
18 APT 0.8765
19 KT4 0.8762
20 J74 0.8757
21 JS7 0.8741
22 J90 0.8724
23 M0V 0.8715
24 IXF 0.8711
25 8VJ 0.8699
26 VXS 0.8689
27 4P9 0.8686
28 2J6 0.8665
29 DTC 0.8655
30 KR5 0.8635
31 OX3 0.8622
32 C3G 0.8617
33 5RX 0.8581
34 QID 0.8577
35 1CE 0.8574
36 41L 0.8567
37 EBB 0.8528
38 B54 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MCC; Ligand: 21X; 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: 4mcc.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4MCC; Ligand: 21X; 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: 4mcc.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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