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 2 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 (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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....
10 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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....
10 1P9P Kd = 68 nM SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 21X; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 21X 1 1
2 21W 0.679487 0.836364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MCC; Ligand: 21X; Similar sites found: 76
This union binding pocket(no: 1) in the query (biounit: 4mcc.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FUI APY 0.01058 0.45296 None
2 5W3Y ACO 0.03067 0.40077 1.21951
3 4RRG A3T 0.002148 0.43303 1.41844
4 4IF4 BEF 0.04339 0.40332 1.44231
5 3OII SAH 0.00001744 0.52016 2.03252
6 1KGZ PRP 0.009924 0.41778 2.03252
7 3WH2 FLC 0.008868 0.44356 2.04082
8 1CT9 AMP 0.005375 0.43985 2.43902
9 2POC UD1 0.009744 0.42666 2.43902
10 1SBR VIB 0.02019 0.4147 2.5
11 1OSS BEN 0.02946 0.40603 2.69058
12 5APG EEM 0.0004882 0.45313 2.7027
13 5UDS ATP 0.006211 0.43203 2.84553
14 3S6X SIA GAL BGC 0.01464 0.41831 2.84553
15 4C2C ALA ALA ALA 0.03018 0.40595 2.84553
16 1RTF BEN 0.01087 0.42911 3.25203
17 3VSE SAH 0.0167 0.4106 3.25203
18 1J1R ADE 0.02854 0.40713 3.25203
19 4BHL ARG 0.02318 0.40328 3.25203
20 3GYQ SAM 0.0001763 0.48122 3.65854
21 2Z9I GLY ALA THR VAL 0.02081 0.41026 3.65854
22 3OF1 CMP 0.02153 0.40507 3.65854
23 5H5F SAM 0.00008883 0.48009 3.84615
24 3BBH SFG 0.000005837 0.55323 3.90244
25 3BBD SAH 0.0001341 0.49156 3.90244
26 1UYY BGC BGC 0.03623 0.40127 4.06504
27 5TVA AMP 0.01723 0.40991 4.16667
28 4JAL SAH 0.0001683 0.42846 4.19162
29 3OCP CMP 0.01977 0.40693 4.31655
30 1KQR MNA 0.0009352 0.4557 4.46927
31 4AU8 Z3R 0.02077 0.40586 4.47154
32 3JUC PCA 0.04392 0.40569 4.47154
33 4I5I 4I5 0.02442 0.40232 4.47154
34 5T52 A2G 0.02852 0.40273 4.54545
35 1GPM AMP 0.007999 0.43095 4.87805
36 3B6O TMP 0.02375 0.41098 4.87805
37 2P3I MNA 0.000278 0.48767 4.96894
38 3RK1 ATP 0.0106 0.41255 5.06329
39 4CNG SAH 0.0007452 0.43262 5.28455
40 5A7Y SAH 0.0002537 0.50736 5.69106
41 2D2F ADP 0.03617 0.40463 5.69106
42 2YY8 MTA 0.00000133 0.60551 5.97015
43 2YY8 SAM 0.0000006884 0.58117 5.97015
44 3U3Z SEP GLN GLU PTR 0.02767 0.40958 6.03015
45 4CNE SAH 0.0003187 0.46981 6.09756
46 4R78 AMP 0.01888 0.41195 6.09756
47 3NK7 SAM 0.0002219 0.47215 6.50407
48 1NE6 SP1 0.009395 0.41136 6.50407
49 1NFU RRP 0.01398 0.41053 6.50407
50 4FXQ G9L 0.03243 0.40557 6.50407
51 2GUC MAN 0.0323 0.40956 6.55738
52 3O7J 2AL 0.0214 0.4052 6.87831
53 4FK7 P34 0.008055 0.436 6.9869
54 2Y7I ARG 0.02447 0.40228 7.86026
55 1TE2 PGA 0.01318 0.4273 7.9646
56 1PVC ILE SER GLU VAL 0.02832 0.42662 7.98319
57 3IWD M2T 0.02023 0.41833 8.06452
58 4JWH SAH 0.000007602 0.51445 8.13008
59 4JWF SAH 0.0000174 0.50473 8.13008
60 3LRE ADP 0.01791 0.41787 8.53659
61 3LE7 ADE 0.03089 0.4041 8.94309
62 2FKA BEF 0.003725 0.45948 9.30233
63 4AUA 4AU 0.01538 0.40139 9.34959
64 3FGZ BEF 0.02476 0.42434 9.375
65 1L7N ALF 0.02288 0.40987 9.47867
66 5AHW CMP 0.005772 0.41748 9.7561
67 3PTG 932 0.003424 0.44984 10.9756
68 3AIA SAM 0.00001557 0.54019 11.3744
69 5TWJ SAM 0.00002178 0.5056 11.7886
70 2IDO TMP 0.02422 0.41334 12.3656
71 1VKF CIT 0.03277 0.40599 12.766
72 2BOS GLA GAL GLC 0.004388 0.45644 16.1765
73 2BOS GLA GAL GLC NBU 0.01282 0.42451 16.1765
74 4XZ3 ACP 0.03291 0.40349 16.2602
75 4JWJ SAH 0.0000177 0.50443 16.3366
76 3HP8 SUC 0.02124 0.41397 25.4545
Pocket No.: 2; Query (leader) PDB : 4MCC; Ligand: 21X; Similar sites found: 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 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback