Receptor
PDB id Resolution Class Description Source Keywords
3EOU 1.93 Å EC: 2.4.2.29 TRNA-GUANINE TRANSGLYCOSYLASE IN COMPLEX WITH 6-AMINO-4-(2- HYDROXYETHYL)-2-(METHYLAMINO)-3,7-DIHYDRO-8H-IMIDAZO[4,5- G ]QUINAZOLIN-8-ONE ZYMOMONAS MOBILIS TIM BARREL GLYCOSYLTRANSFERASE METAL-BINDING QUEUOSINE 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:600;
A:601;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PK3 A:500;
Valid;
none;
Ki = 97 nM
274.279 C12 H14 N6 O2 CNc1[...
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: PK3; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 PK3 1 1
2 2MQ 0.80303 0.881356
3 1WK 0.412371 0.791045
4 AEK 0.408602 0.793651
5 2WU 0.402597 0.789474
Similar Ligands (3D)
Ligand no: 1; Ligand: PK3; Similar ligands found: 76
No: Ligand Similarity coefficient
1 EAE 0.9218
2 VUP 0.9121
3 Z21 0.9101
4 8MO 0.9090
5 CQO 0.9079
6 ZO9 0.9057
7 ALH 0.9039
8 S98 0.9031
9 LFN 0.9029
10 3E2 0.8972
11 9OF 0.8952
12 M3F 0.8941
13 2AN 0.8929
14 9GT 0.8919
15 GO1 0.8910
16 Z73 0.8901
17 S60 0.8889
18 BGU 0.8879
19 HRD 0.8876
20 9GW 0.8861
21 ITE 0.8839
22 EI1 0.8839
23 ZSP 0.8830
24 EMO 0.8826
25 COL 0.8820
26 H4B 0.8802
27 6FV 0.8798
28 BFH 0.8793
29 57Q 0.8791
30 N0Z 0.8781
31 OTA 0.8780
32 AXX 0.8778
33 RHN 0.8771
34 IRG 0.8763
35 3J8 0.8758
36 IXM 0.8756
37 E1K 0.8734
38 K7H 0.8734
39 NOM 0.8717
40 DX2 0.8717
41 5OR 0.8717
42 1DR 0.8715
43 761 0.8713
44 OPA 0.8712
45 9TF 0.8701
46 LUM 0.8700
47 H05 0.8699
48 Z80 0.8695
49 EED 0.8674
50 EES 0.8670
51 0CV 0.8666
52 3C3 0.8662
53 537 0.8646
54 IQZ 0.8632
55 9GN 0.8626
56 JWS 0.8614
57 HRM 0.8611
58 B56 0.8610
59 DX7 0.8606
60 B61 0.8601
61 6O3 0.8598
62 22T 0.8594
63 NRA 0.8592
64 OAI 0.8588
65 THA 0.8583
66 H2B 0.8579
67 8SK 0.8579
68 BIO 0.8575
69 YZ9 0.8570
70 P57 0.8559
71 K66 0.8555
72 4E3 0.8553
73 TXQ 0.8542
74 PRL 0.8522
75 H5B 0.8522
76 19E 0.8513
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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