Receptor
PDB id Resolution Class Description Source Keywords
3GC5 1.4 Å EC: 2.4.2.29 TRNA-GUANINE TRANSGLYCOSYLASE IN COMPLEX WITH 6-AMINO-4-(2- AMINOETHYL)-2-(METHYLAMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QU8 -ONE ZYMOMONAS MOBILIS DRUG DESIGN TIM BARREL TRNA MODIFICATION GLYCOSYLTRANSFERMETAL-BINDING QUEUOSINE BIOSYNTHESIS TRANSFERASE TRNA PR
Ref.: HOW TO REPLACE THE RESIDUAL SOLVATION SHELL OF POLA SITE RESIDUES TO ACHIEVE NANOMOLAR INHIBITION OF TRNA-GUANINE TRANSGLYCOSYLASE CHEMMEDCHEM V. 4 2012 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2MQ A:400;
 Valid;
 none;
 Ki = 55 nM
273.294 C12 H15 N7 O CNc1[...
GOL A:401;
A:402;
A:403;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
ZN A:390;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GE7 1.5 Å EC: 2.4.2.29 TRNA-GUANINE TRANSGLYCOSYLASE IN COMPLEX WITH 6-AMINO-4-{2- [(CYCLOPENTYLMETHYL)AMINO]ETHYL}-2-(METHYLAMINO)-1,7-DIHYDRI MIDAZO[4,5-G]QUINAZOLIN-8-ONE ZYMOMONAS MOBILIS DRUG DESIGN TGT TIM BARREL GLYCOSYLTRANSFERASE METAL-BINDQUEUOSINE BIOSYNTHESIS TRANSFERASE TRNA PROCESSING
Ref.: HOW TO REPLACE THE RESIDUAL SOLVATION SHELL OF POLA SITE RESIDUES TO ACHIEVE NANOMOLAR INHIBITION OF TRNA-GUANINE TRANSGLYCOSYLASE CHEMMEDCHEM V. 4 2012 2009
Members (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1ENU Ki = 8.3 uM APZ C8 H7 N3 O2 c1cc2c(cc1....
2 2PWU - GUN C5 H5 N5 O c1[nH]c2c(....
3 4Q4S Kd = 111.6 nM S98 C14 H12 N6 O S c1cc(sc1)C....
4 2QII - PQ0 C7 H5 N5 O c1c(c2c([n....
5 1PXG - PRF C7 H9 N5 O c1c(c2c([n....
6 4KWO Ki = 353 nM 1UD C18 H24 N6 O5 CNc1[nH]c2....
7 2Z7K Ki = 77 nM BGU C9 H8 N6 O c1c2c(cc3c....
8 3SM0 Ki = 740 nM AEK C18 H24 N6 O CNc1[nH]c2....
9 6RKQ Ki = 48 uM K75 C13 H14 N6 CC#C[C@@H]....
10 4Q4P Kd = 407.4 nM 2YO C16 H20 N6 O c1c2c(cc3c....
11 1K4H Ki = 7.7 uM APQ C12 H16 N4 O S CCCSCc1cc(....
12 1EFZ - PRF C7 H9 N5 O c1c(c2c([n....
13 3C2Y Ki = 1.5 uM S60 C10 H9 N5 O Cc1[nH]c2c....
14 1Y5X Ki = 3.7 uM E89 C18 H17 N5 O2 COc1ccc(cc....
15 1R5Y Ki = 0.35 uM DQU C8 H8 N4 O c1cc2c(cc1....
16 3RR4 Ki = 28050 nM HRD C11 H12 N6 O CNc1[nH]c2....
17 3EOU Ki = 97 nM PK3 C12 H14 N6 O2 CNc1[nH]c2....
18 6FMN Kd = 1120 nM E4E C15 H18 N6 O5 CO[C@H]1[C....
19 4Q4Q Kd = 1638.9 nM SAQ C14 H11 N5 O S c1cc(sc1)C....
20 4E2V - PRF C7 H9 N5 O c1c(c2c([n....
21 2Z1X - PRF C7 H9 N5 O c1c(c2c([n....
22 5JXQ Ki = 7 nM 6OK C19 H20 N6 O2 c1cc(ccc1C....
23 1Q66 Ki = 1.7 uM KMB C16 H16 N4 O S c1ccc(cc1)....
24 1N2V Ki = 83 uM BDI C9 H12 N4 O2 CCCCc1[nH]....
25 1Y5W Ki = 6.9 uM NEZ C18 H17 N5 O Cc1ccc(cc1....
26 1Q63 Ki = 1.4 uM AIQ C12 H12 N6 O S c1cnc([nH]....
27 4PUL Kd = 146.1 nM 2WU C10 H10 N6 O CNc1[nH]c2....
28 3GC4 Ki = 25 nM AAQ C19 H21 N7 O CNc1[nH]c2....
29 4LBU Kd = 276 nM 1WJ C18 H24 N6 O5 CNc1[nH]c2....
30 6RKT Ki = 17 uM K7H C10 H12 N6 CNc1[nH]c2....
31 2Z1W - BDI C9 H12 N4 O2 CCCCc1[nH]....
32 1K4G Ki = 1.4 uM AIQ C12 H12 N6 O S c1cnc([nH]....
33 1P0E - PRF C7 H9 N5 O c1c(c2c([n....
34 4LEQ Kd = 288 nM 1WK C17 H22 N6 O5 CNc1[nH]c2....
35 1P0B - PQ0 C7 H5 N5 O c1c(c2c([n....
36 2POT - GUN C5 H5 N5 O c1[nH]c2c(....
37 2QZR Ki = 55 nM S79 C20 H16 N6 O c1ccc2c(c1....
38 4Q4O Kd = 34.3 nM 2YM C16 H21 N7 O c1c2c(cc3c....
39 3S1G Ki = 6500 nM ITE C10 H9 N5 O CNc1[nH]c2....
40 4PUM Kd = 188.1 nM 2WU C10 H10 N6 O CNc1[nH]c2....
41 1S38 Ki = 7 uM MAQ C9 H9 N3 O Cc1cccc2c1....
42 1Q65 Ki = 3.5 uM BHB C13 H19 N5 O S CN(C)CCSCc....
43 3EOS Ki = 4 nM PK2 C19 H27 N7 O CNc1[nH]c2....
44 1F3E Ki = 0.2 uM DPZ C8 H8 N4 O2 c1c(cc(c2c....
45 1Y5V Ki = 1 uM NE8 C17 H15 N5 O c1ccc(cc1)....
46 1OZQ - PRF C7 H9 N5 O c1c(c2c([n....
47 4PUJ Kd = 35 nM CKR C15 H19 N7 O2 c1c2c(cc3c....
48 2BBF Ki = 7.9 uM 344 C9 H7 N5 O c1c2c(cc3c....
49 6FPU Kd = 321 nM E48 C21 H26 N6 O6 CC1(O[C@@H....
50 1S39 Ki = 20 nM AQO C8 H7 N3 O c1ccc2c(c1....
51 3TLL Ki = 40830 nM 62D C12 H14 N6 O CCNC1=Nc2c....
52 4PUK Kd = 52.4 nM 2WU C10 H10 N6 O CNc1[nH]c2....
53 2PWV - PQ0 C7 H5 N5 O c1c(c2c([n....
54 3GC5 Ki = 55 nM 2MQ C12 H15 N7 O CNc1[nH]c2....
55 3GE7 Ki = 2 nM AFQ C18 H25 N7 O CNc1[nH]c2....
56 4Q4R Kd = 369.2 nM SQO C15 H18 N6 O2 c1c2c(cc3c....
57 1Q4W Ki = 0.35 uM DQU C8 H8 N4 O c1cc2c(cc1....
70% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1ENU Ki = 8.3 uM APZ C8 H7 N3 O2 c1cc2c(cc1....
2 2PWU - GUN C5 H5 N5 O c1[nH]c2c(....
3 4Q4S Kd = 111.6 nM S98 C14 H12 N6 O S c1cc(sc1)C....
4 2QII - PQ0 C7 H5 N5 O c1c(c2c([n....
5 1PXG - PRF C7 H9 N5 O c1c(c2c([n....
6 4KWO Ki = 353 nM 1UD C18 H24 N6 O5 CNc1[nH]c2....
7 2Z7K Ki = 77 nM BGU C9 H8 N6 O c1c2c(cc3c....
8 3SM0 Ki = 740 nM AEK C18 H24 N6 O CNc1[nH]c2....
9 6RKQ Ki = 48 uM K75 C13 H14 N6 CC#C[C@@H]....
10 4Q4P Kd = 407.4 nM 2YO C16 H20 N6 O c1c2c(cc3c....
11 1K4H Ki = 7.7 uM APQ C12 H16 N4 O S CCCSCc1cc(....
12 1EFZ - PRF C7 H9 N5 O c1c(c2c([n....
13 3C2Y Ki = 1.5 uM S60 C10 H9 N5 O Cc1[nH]c2c....
14 1Y5X Ki = 3.7 uM E89 C18 H17 N5 O2 COc1ccc(cc....
15 1R5Y Ki = 0.35 uM DQU C8 H8 N4 O c1cc2c(cc1....
16 3RR4 Ki = 28050 nM HRD C11 H12 N6 O CNc1[nH]c2....
17 3EOU Ki = 97 nM PK3 C12 H14 N6 O2 CNc1[nH]c2....
18 6FMN Kd = 1120 nM E4E C15 H18 N6 O5 CO[C@H]1[C....
19 4Q4Q Kd = 1638.9 nM SAQ C14 H11 N5 O S c1cc(sc1)C....
20 4E2V - PRF C7 H9 N5 O c1c(c2c([n....
21 2Z1X - PRF C7 H9 N5 O c1c(c2c([n....
22 5JXQ Ki = 7 nM 6OK C19 H20 N6 O2 c1cc(ccc1C....
23 1Q66 Ki = 1.7 uM KMB C16 H16 N4 O S c1ccc(cc1)....
24 1N2V Ki = 83 uM BDI C9 H12 N4 O2 CCCCc1[nH]....
25 1Y5W Ki = 6.9 uM NEZ C18 H17 N5 O Cc1ccc(cc1....
26 1Q63 Ki = 1.4 uM AIQ C12 H12 N6 O S c1cnc([nH]....
27 4PUL Kd = 146.1 nM 2WU C10 H10 N6 O CNc1[nH]c2....
28 3GC4 Ki = 25 nM AAQ C19 H21 N7 O CNc1[nH]c2....
29 4LBU Kd = 276 nM 1WJ C18 H24 N6 O5 CNc1[nH]c2....
30 6RKT Ki = 17 uM K7H C10 H12 N6 CNc1[nH]c2....
31 2Z1W - BDI C9 H12 N4 O2 CCCCc1[nH]....
32 1K4G Ki = 1.4 uM AIQ C12 H12 N6 O S c1cnc([nH]....
33 1P0E - PRF C7 H9 N5 O c1c(c2c([n....
34 4LEQ Kd = 288 nM 1WK C17 H22 N6 O5 CNc1[nH]c2....
35 1P0B - PQ0 C7 H5 N5 O c1c(c2c([n....
36 2POT - GUN C5 H5 N5 O c1[nH]c2c(....
37 2QZR Ki = 55 nM S79 C20 H16 N6 O c1ccc2c(c1....
38 4Q4O Kd = 34.3 nM 2YM C16 H21 N7 O c1c2c(cc3c....
39 3S1G Ki = 6500 nM ITE C10 H9 N5 O CNc1[nH]c2....
40 4PUM Kd = 188.1 nM 2WU C10 H10 N6 O CNc1[nH]c2....
41 1S38 Ki = 7 uM MAQ C9 H9 N3 O Cc1cccc2c1....
42 1Q65 Ki = 3.5 uM BHB C13 H19 N5 O S CN(C)CCSCc....
43 3EOS Ki = 4 nM PK2 C19 H27 N7 O CNc1[nH]c2....
44 1F3E Ki = 0.2 uM DPZ C8 H8 N4 O2 c1c(cc(c2c....
45 1Y5V Ki = 1 uM NE8 C17 H15 N5 O c1ccc(cc1)....
46 1OZQ - PRF C7 H9 N5 O c1c(c2c([n....
47 4PUJ Kd = 35 nM CKR C15 H19 N7 O2 c1c2c(cc3c....
48 2BBF Ki = 7.9 uM 344 C9 H7 N5 O c1c2c(cc3c....
49 6FPU Kd = 321 nM E48 C21 H26 N6 O6 CC1(O[C@@H....
50 1S39 Ki = 20 nM AQO C8 H7 N3 O c1ccc2c(c1....
51 3TLL Ki = 40830 nM 62D C12 H14 N6 O CCNC1=Nc2c....
52 4PUK Kd = 52.4 nM 2WU C10 H10 N6 O CNc1[nH]c2....
53 2PWV - PQ0 C7 H5 N5 O c1c(c2c([n....
54 3GC5 Ki = 55 nM 2MQ C12 H15 N7 O CNc1[nH]c2....
55 3GE7 Ki = 2 nM AFQ C18 H25 N7 O CNc1[nH]c2....
56 4Q4R Kd = 369.2 nM SQO C15 H18 N6 O2 c1c2c(cc3c....
57 1Q4W Ki = 0.35 uM DQU C8 H8 N4 O c1cc2c(cc1....
50% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1ENU Ki = 8.3 uM APZ C8 H7 N3 O2 c1cc2c(cc1....
2 2PWU - GUN C5 H5 N5 O c1[nH]c2c(....
3 4Q4S Kd = 111.6 nM S98 C14 H12 N6 O S c1cc(sc1)C....
4 2QII - PQ0 C7 H5 N5 O c1c(c2c([n....
5 1PXG - PRF C7 H9 N5 O c1c(c2c([n....
6 4KWO Ki = 353 nM 1UD C18 H24 N6 O5 CNc1[nH]c2....
7 2Z7K Ki = 77 nM BGU C9 H8 N6 O c1c2c(cc3c....
8 3SM0 Ki = 740 nM AEK C18 H24 N6 O CNc1[nH]c2....
9 6RKQ Ki = 48 uM K75 C13 H14 N6 CC#C[C@@H]....
10 4Q4P Kd = 407.4 nM 2YO C16 H20 N6 O c1c2c(cc3c....
11 1K4H Ki = 7.7 uM APQ C12 H16 N4 O S CCCSCc1cc(....
12 1EFZ - PRF C7 H9 N5 O c1c(c2c([n....
13 3C2Y Ki = 1.5 uM S60 C10 H9 N5 O Cc1[nH]c2c....
14 1Y5X Ki = 3.7 uM E89 C18 H17 N5 O2 COc1ccc(cc....
15 1R5Y Ki = 0.35 uM DQU C8 H8 N4 O c1cc2c(cc1....
16 3RR4 Ki = 28050 nM HRD C11 H12 N6 O CNc1[nH]c2....
17 3EOU Ki = 97 nM PK3 C12 H14 N6 O2 CNc1[nH]c2....
18 6FMN Kd = 1120 nM E4E C15 H18 N6 O5 CO[C@H]1[C....
19 4Q4Q Kd = 1638.9 nM SAQ C14 H11 N5 O S c1cc(sc1)C....
20 4E2V - PRF C7 H9 N5 O c1c(c2c([n....
21 2Z1X - PRF C7 H9 N5 O c1c(c2c([n....
22 5JXQ Ki = 7 nM 6OK C19 H20 N6 O2 c1cc(ccc1C....
23 1Q66 Ki = 1.7 uM KMB C16 H16 N4 O S c1ccc(cc1)....
24 1N2V Ki = 83 uM BDI C9 H12 N4 O2 CCCCc1[nH]....
25 1Y5W Ki = 6.9 uM NEZ C18 H17 N5 O Cc1ccc(cc1....
26 1Q63 Ki = 1.4 uM AIQ C12 H12 N6 O S c1cnc([nH]....
27 4PUL Kd = 146.1 nM 2WU C10 H10 N6 O CNc1[nH]c2....
28 3GC4 Ki = 25 nM AAQ C19 H21 N7 O CNc1[nH]c2....
29 4LBU Kd = 276 nM 1WJ C18 H24 N6 O5 CNc1[nH]c2....
30 6RKT Ki = 17 uM K7H C10 H12 N6 CNc1[nH]c2....
31 2Z1W - BDI C9 H12 N4 O2 CCCCc1[nH]....
32 1K4G Ki = 1.4 uM AIQ C12 H12 N6 O S c1cnc([nH]....
33 1P0E - PRF C7 H9 N5 O c1c(c2c([n....
34 4LEQ Kd = 288 nM 1WK C17 H22 N6 O5 CNc1[nH]c2....
35 1P0B - PQ0 C7 H5 N5 O c1c(c2c([n....
36 2POT - GUN C5 H5 N5 O c1[nH]c2c(....
37 2QZR Ki = 55 nM S79 C20 H16 N6 O c1ccc2c(c1....
38 4Q4O Kd = 34.3 nM 2YM C16 H21 N7 O c1c2c(cc3c....
39 3S1G Ki = 6500 nM ITE C10 H9 N5 O CNc1[nH]c2....
40 4PUM Kd = 188.1 nM 2WU C10 H10 N6 O CNc1[nH]c2....
41 1S38 Ki = 7 uM MAQ C9 H9 N3 O Cc1cccc2c1....
42 1Q65 Ki = 3.5 uM BHB C13 H19 N5 O S CN(C)CCSCc....
43 3EOS Ki = 4 nM PK2 C19 H27 N7 O CNc1[nH]c2....
44 1F3E Ki = 0.2 uM DPZ C8 H8 N4 O2 c1c(cc(c2c....
45 1Y5V Ki = 1 uM NE8 C17 H15 N5 O c1ccc(cc1)....
46 1OZQ - PRF C7 H9 N5 O c1c(c2c([n....
47 4PUJ Kd = 35 nM CKR C15 H19 N7 O2 c1c2c(cc3c....
48 2BBF Ki = 7.9 uM 344 C9 H7 N5 O c1c2c(cc3c....
49 6FPU Kd = 321 nM E48 C21 H26 N6 O6 CC1(O[C@@H....
50 1S39 Ki = 20 nM AQO C8 H7 N3 O c1ccc2c(c1....
51 3TLL Ki = 40830 nM 62D C12 H14 N6 O CCNC1=Nc2c....
52 4PUK Kd = 52.4 nM 2WU C10 H10 N6 O CNc1[nH]c2....
53 2PWV - PQ0 C7 H5 N5 O c1c(c2c([n....
54 3GC5 Ki = 55 nM 2MQ C12 H15 N7 O CNc1[nH]c2....
55 3GE7 Ki = 2 nM AFQ C18 H25 N7 O CNc1[nH]c2....
56 4Q4R Kd = 369.2 nM SQO C15 H18 N6 O2 c1c2c(cc3c....
57 1Q4W Ki = 0.35 uM DQU C8 H8 N4 O c1cc2c(cc1....
58 6H42 - GGL C5 H9 N O4 C(CC(=O)O)....
59 6H45 - QEI C12 H15 N5 O3 c1c(c2c([n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 2MQ; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 2MQ 1 1
2 PK3 0.80303 0.881356
3 AFQ 0.430108 0.931035
4 AEK 0.428571 0.896552
5 PK2 0.421053 0.931035
6 AAQ 0.410526 0.946429
7 2WU 0.407895 0.833333
8 1WK 0.402062 0.720588
Similar Ligands (3D)
Ligand no: 1; Ligand: 2MQ; Similar ligands found: 59
No: Ligand Similarity coefficient
1 EAE 0.9177
2 VUP 0.9118
3 Z21 0.9067
4 8MO 0.9046
5 3E2 0.9038
6 S98 0.9005
7 ZO9 0.8983
8 CQO 0.8973
9 LFN 0.8945
10 GO1 0.8941
11 ALH 0.8938
12 S60 0.8873
13 M3F 0.8866
14 HRD 0.8857
15 9GT 0.8856
16 6FV 0.8855
17 2AN 0.8855
18 BGU 0.8852
19 H4B 0.8833
20 9GW 0.8818
21 AXX 0.8814
22 ZSP 0.8814
23 ITE 0.8807
24 EI1 0.8800
25 Z73 0.8798
26 EMO 0.8791
27 LUM 0.8767
28 BFH 0.8766
29 E1K 0.8766
30 1DR 0.8762
31 OTA 0.8760
32 N0Z 0.8750
33 OPA 0.8736
34 3J8 0.8734
35 K7H 0.8732
36 COL 0.8731
37 RHN 0.8714
38 0CV 0.8709
39 5OR 0.8703
40 EES 0.8695
41 IXM 0.8670
42 DX2 0.8668
43 9TF 0.8657
44 3C3 0.8649
45 6O3 0.8632
46 Z80 0.8632
47 H05 0.8625
48 NOM 0.8625
49 IQZ 0.8621
50 EED 0.8614
51 DX7 0.8604
52 OAI 0.8599
53 761 0.8595
54 B56 0.8595
55 537 0.8583
56 THA 0.8560
57 BIO 0.8546
58 BA5 0.8530
59 YZ9 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GE7; Ligand: AFQ; 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: 3ge7.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3GE7; Ligand: AFQ; 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: 3ge7.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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