Receptor
PDB id Resolution Class Description Source Keywords
2GG5 2.12 Å EC: 3.4.11.18 NOVEL BACTERIAL METHIONINE AMINOPEPTIDASE INHIBITORS ESCHERICHIA COLI K12 METHIONINE AMINO PEPTIDASE PITA-BREAD FOLD MAP INHIBITOR ANTIBACTERIAL HYDROLASE
Ref.: SERENDIPITOUS DISCOVERY OF NOVEL BACTERIAL METHIONI AMINOPEPTIDASE INHIBITORS. PROTEINS V. 66 538 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:301;
A:302;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
58.933 Co [Co+2...
NA A:503;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
U19 A:501;
 Valid;
 none;
 ic50 = 0.25 uM
268.198 C10 H7 F3 N6 [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YVM 1.6 Å EC: 3.4.11.18 E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH THIABENDAZOLE ESCHERICHIA COLI HYDROLASE(ALPHA-AMINOACYLPEPTIDE) METAL COMPLEX THIABENDAZOLE METHIONINE AMINOPEPTIDASE INHIBITOR
Ref.: METAL IONS AS COFACTORS FOR THE BINDING OF INHIBITORS TO METHIONINE AMINOPEPTIDASE: A CRITICAL VIEW OF THE RELEVANCE OF IN VITRO METALLOENZYME ASSAYS. ANGEW.CHEM.INT.ED.ENGL. V. 44 3620 2005
Members (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2GG0 ic50 = 1.7 uM U11 C16 H20 F3 N3 O5 C[C@@H](C(....
2 1YVM Ki = 0.4 uM TMG C10 H7 N3 S c1ccc2c(c1....
3 2GU6 - NLP C5 H14 N O3 P CCCC[C@H](....
4 2Q95 ic50 = 1.6 uM A05 C11 H6 Cl N O5 c1cc(c(cc1....
5 2GG8 ic50 = 25 uM U15 C20 H31 N3 O5 Cc1ccc(cc1....
6 2GTX - NLP C5 H14 N O3 P CCCC[C@H](....
7 2EVC ic50 = 0.29 uM FC3 C12 H7 F3 O3 c1ccc(c(c1....
8 4A6W ic50 = 1.9 uM 5C1 C10 H7 Cl N2 O3 c1ccc(c(c1....
9 2GG3 ic50 = 0.58 uM U13 C9 H7 F N6 [H]/N=C/1C....
10 3D27 ic50 = 55.7 uM W29 C12 H12 O2 S CCc1ccsc1c....
11 2GG7 ic50 = 1.75 uM U14 C10 H8 N6 O2 [H]/N=C1/C....
12 2GU5 - NLP C5 H14 N O3 P CCCC[C@H](....
13 1XNZ ic50 = 0.24 uM FCD C11 H7 Cl O3 c1ccc(c(c1....
14 4A6V ic50 = 1.9 uM IKY C11 H7 F3 N2 O3 c1ccc(c(c1....
15 1C21 - MET C5 H11 N O2 S CSCC[C@@H]....
16 2Q92 ic50 = 1.1 uM B23 C11 H7 N O5 c1ccc(c(c1....
17 1C27 - NLP C5 H14 N O3 P CCCC[C@H](....
18 1C24 - MPJ C4 H12 N O2 P S CSCC[C@H](....
19 2EVO ic50 = 0.067 uM CT0 C10 H13 N3 O2 S c1csc(n1)N....
20 2P99 ic50 = 1.16 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
21 2GG9 ic50 = 3.5 uM U16 C22 H35 N3 O5 CC(C)C[C@H....
22 2Q94 ic50 = 0.37 uM A04 C12 H7 F3 O4 c1ccc(c(c1....
23 2P98 ic50 = 0.64 uM YE7 C12 H10 N4 O c1ccc2c(c1....
24 2GGB ic50 = 12 uM U17 C17 H33 N3 O6 CCCC[C@H](....
25 2EVM ic50 = 0.693 uM FC2 C11 H6 Cl2 O3 c1cc(c(cc1....
26 1C22 - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
27 1C23 - MPH C4 H12 N O3 P S CSCC[C@H](....
28 2Q96 ic50 = 1.2 uM A18 C12 H9 Cl O3 c1ccc(c(c1....
29 2BB7 ic50 = 2.14 uM QMS C10 H10 N2 O2 S CS(=O)(=O)....
30 2GG2 ic50 = 0.25 uM U12 C10 H7 F3 N6 c1cc(cc(c1....
31 2GGC - MET C5 H11 N O2 S CSCC[C@@H]....
32 2GU4 - NLP C5 H14 N O3 P CCCC[C@H](....
33 2Q93 ic50 = 0.56 uM B21 C12 H10 O4 COc1ccccc1....
34 2GG5 ic50 = 0.25 uM U19 C10 H7 F3 N6 [H]/N=C1/C....
35 3MAT - AHH ALA LEU VAL 0A9 n/a n/a
36 2P9A ic50 = 6.56 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2GG0 ic50 = 1.7 uM U11 C16 H20 F3 N3 O5 C[C@@H](C(....
2 1YVM Ki = 0.4 uM TMG C10 H7 N3 S c1ccc2c(c1....
3 2GU6 - NLP C5 H14 N O3 P CCCC[C@H](....
4 2Q95 ic50 = 1.6 uM A05 C11 H6 Cl N O5 c1cc(c(cc1....
5 2GG8 ic50 = 25 uM U15 C20 H31 N3 O5 Cc1ccc(cc1....
6 2GTX - NLP C5 H14 N O3 P CCCC[C@H](....
7 2EVC ic50 = 0.29 uM FC3 C12 H7 F3 O3 c1ccc(c(c1....
8 4A6W ic50 = 1.9 uM 5C1 C10 H7 Cl N2 O3 c1ccc(c(c1....
9 2GG3 ic50 = 0.58 uM U13 C9 H7 F N6 [H]/N=C/1C....
10 3D27 ic50 = 55.7 uM W29 C12 H12 O2 S CCc1ccsc1c....
11 2GG7 ic50 = 1.75 uM U14 C10 H8 N6 O2 [H]/N=C1/C....
12 2GU5 - NLP C5 H14 N O3 P CCCC[C@H](....
13 1XNZ ic50 = 0.24 uM FCD C11 H7 Cl O3 c1ccc(c(c1....
14 4A6V ic50 = 1.9 uM IKY C11 H7 F3 N2 O3 c1ccc(c(c1....
15 1C21 - MET C5 H11 N O2 S CSCC[C@@H]....
16 2Q92 ic50 = 1.1 uM B23 C11 H7 N O5 c1ccc(c(c1....
17 1C27 - NLP C5 H14 N O3 P CCCC[C@H](....
18 1C24 - MPJ C4 H12 N O2 P S CSCC[C@H](....
19 2EVO ic50 = 0.067 uM CT0 C10 H13 N3 O2 S c1csc(n1)N....
20 2P99 ic50 = 1.16 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
21 2GG9 ic50 = 3.5 uM U16 C22 H35 N3 O5 CC(C)C[C@H....
22 2Q94 ic50 = 0.37 uM A04 C12 H7 F3 O4 c1ccc(c(c1....
23 2P98 ic50 = 0.64 uM YE7 C12 H10 N4 O c1ccc2c(c1....
24 2GGB ic50 = 12 uM U17 C17 H33 N3 O6 CCCC[C@H](....
25 2EVM ic50 = 0.693 uM FC2 C11 H6 Cl2 O3 c1cc(c(cc1....
26 1C22 - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
27 1C23 - MPH C4 H12 N O3 P S CSCC[C@H](....
28 2Q96 ic50 = 1.2 uM A18 C12 H9 Cl O3 c1ccc(c(c1....
29 2BB7 ic50 = 2.14 uM QMS C10 H10 N2 O2 S CS(=O)(=O)....
30 2GG2 ic50 = 0.25 uM U12 C10 H7 F3 N6 c1cc(cc(c1....
31 2GGC - MET C5 H11 N O2 S CSCC[C@@H]....
32 2GU4 - NLP C5 H14 N O3 P CCCC[C@H](....
33 2Q93 ic50 = 0.56 uM B21 C12 H10 O4 COc1ccccc1....
34 2GG5 ic50 = 0.25 uM U19 C10 H7 F3 N6 [H]/N=C1/C....
35 3MAT - AHH ALA LEU VAL 0A9 n/a n/a
36 2P9A ic50 = 6.56 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
50% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2NQ6 ic50 = 1.5 uM HM4 C14 H16 N4 O3 S CC(C)(C)OC....
2 4U69 Ki = 54.8 uM Q07 C6 H16 N O3 P CCC[C@H](C....
3 2G6P ic50 = 0.6 uM HM2 C18 H17 Cl N4 Cc1c(c(nc(....
4 4U73 Ki = 6.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
5 4IKT ic50 = 0.67 uM TFV C18 H16 Cl F3 N6 Cc1c(c(nc(....
6 4U6Z Ki = 3.9 uM Q07 C6 H16 N O3 P CCC[C@H](C....
7 4U70 Ki = 9.5 uM Q04 C8 H18 N O3 P C1CCC(CC1)....
8 4FLI ic50 = 3.59 uM Y16 C14 H26 N2 O6 CC(C)(C)/C....
9 4U6C Ki = 9.9 uM Q06 C8 H18 N O3 P C1CCC(C1)C....
10 4IKR ic50 = 0.59 uM PVP C16 H20 Cl N5 O Cc1c(c(nc(....
11 4FLK ic50 = 5.58 uM Y10 C21 H31 N O5 CC(C)(C)/C....
12 4IKU ic50 = 1.79 uM SHX C19 H18 Cl N5 O Cc1c(c(nc(....
13 2NQ7 ic50 = 2.9 uM HM5 C14 H16 N4 O2 S CC(C)(C)C(....
14 4FLL ic50 = 5.14 uM YZ6 C25 H35 N O6 CC(C)(C)/C....
15 4U71 Ki = 6 uM Q03 C7 H16 N O3 P C1CCC(CC1)....
16 4HXX - 1AY C28 H29 Cl2 N5 Cc1c(c(nc(....
17 4IKS ic50 = 7.23 uM TFD C18 H16 Cl F3 N6 Cc1c(c(nc(....
18 4U6E Ki = 111.6 uM Q02 C7 H10 N O3 P c1ccc(cc1)....
19 4U1B Ki = 4.9 uM Q08 C8 H20 N O3 P CCCC(CCC)[....
20 4FLJ ic50 = 7.45 uM Y08 C22 H38 N2 O6 CC(C)(C)/C....
21 2GG0 ic50 = 1.7 uM U11 C16 H20 F3 N3 O5 C[C@@H](C(....
22 1YVM Ki = 0.4 uM TMG C10 H7 N3 S c1ccc2c(c1....
23 2GU6 - NLP C5 H14 N O3 P CCCC[C@H](....
24 2Q95 ic50 = 1.6 uM A05 C11 H6 Cl N O5 c1cc(c(cc1....
25 2GG8 ic50 = 25 uM U15 C20 H31 N3 O5 Cc1ccc(cc1....
26 2GTX - NLP C5 H14 N O3 P CCCC[C@H](....
27 2EVC ic50 = 0.29 uM FC3 C12 H7 F3 O3 c1ccc(c(c1....
28 4A6W ic50 = 1.9 uM 5C1 C10 H7 Cl N2 O3 c1ccc(c(c1....
29 2GG3 ic50 = 0.58 uM U13 C9 H7 F N6 [H]/N=C/1C....
30 3D27 ic50 = 55.7 uM W29 C12 H12 O2 S CCc1ccsc1c....
31 2GG7 ic50 = 1.75 uM U14 C10 H8 N6 O2 [H]/N=C1/C....
32 2GU5 - NLP C5 H14 N O3 P CCCC[C@H](....
33 1XNZ ic50 = 0.24 uM FCD C11 H7 Cl O3 c1ccc(c(c1....
34 4A6V ic50 = 1.9 uM IKY C11 H7 F3 N2 O3 c1ccc(c(c1....
35 1C21 - MET C5 H11 N O2 S CSCC[C@@H]....
36 2Q92 ic50 = 1.1 uM B23 C11 H7 N O5 c1ccc(c(c1....
37 1C27 - NLP C5 H14 N O3 P CCCC[C@H](....
38 1C24 - MPJ C4 H12 N O2 P S CSCC[C@H](....
39 2EVO ic50 = 0.067 uM CT0 C10 H13 N3 O2 S c1csc(n1)N....
40 2P99 ic50 = 1.16 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
41 2GG9 ic50 = 3.5 uM U16 C22 H35 N3 O5 CC(C)C[C@H....
42 2Q94 ic50 = 0.37 uM A04 C12 H7 F3 O4 c1ccc(c(c1....
43 2P98 ic50 = 0.64 uM YE7 C12 H10 N4 O c1ccc2c(c1....
44 2GGB ic50 = 12 uM U17 C17 H33 N3 O6 CCCC[C@H](....
45 2EVM ic50 = 0.693 uM FC2 C11 H6 Cl2 O3 c1cc(c(cc1....
46 1C22 - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
47 1C23 - MPH C4 H12 N O3 P S CSCC[C@H](....
48 2Q96 ic50 = 1.2 uM A18 C12 H9 Cl O3 c1ccc(c(c1....
49 2BB7 ic50 = 2.14 uM QMS C10 H10 N2 O2 S CS(=O)(=O)....
50 2GG2 ic50 = 0.25 uM U12 C10 H7 F3 N6 c1cc(cc(c1....
51 2GGC - MET C5 H11 N O2 S CSCC[C@@H]....
52 2GU4 - NLP C5 H14 N O3 P CCCC[C@H](....
53 2Q93 ic50 = 0.56 uM B21 C12 H10 O4 COc1ccccc1....
54 2GG5 ic50 = 0.25 uM U19 C10 H7 F3 N6 [H]/N=C1/C....
55 3MAT - AHH ALA LEU VAL 0A9 n/a n/a
56 2P9A ic50 = 6.56 uM YE6 C11 H9 Cl N2 O2 c1ccc(c(c1....
57 4IU6 - FZ1 C24 H23 N5 O COc1ccc(cc....
58 1QXZ ic50 = 19 uM M3C C8 H14 N2 O2 S2 CSCC[C@@H]....
59 1QXY ic50 = 16 uM M2C C10 H16 N2 O2 S CSCC[C@@H]....
60 1QXW ic50 = 7 uM M1C C10 H22 N2 O2 CCCC[C@@H]....
61 3IU9 ic50 = 0.24 uM T07 C9 H8 Cl2 N4 S c1cc(c(cc1....
62 3IU7 ic50 = 16 uM FCD C11 H7 Cl O3 c1ccc(c(c1....
63 3PKE - Y10 C21 H31 N O5 CC(C)(C)/C....
64 3PKB ic50 = 0.62 uM Y16 C14 H26 N2 O6 CC(C)(C)/C....
65 3PKA ic50 = 0.54 uM Y02 C23 H37 N O6 Cc1cc(c(c(....
66 3PKC ic50 = 0.96 uM Y08 C22 H38 N2 O6 CC(C)(C)/C....
67 3IU8 ic50 = 0.58 uM T03 C9 H8 F N3 S c1cc(ccc1C....
68 3PKD ic50 = 0.76 uM Y10 C21 H31 N O5 CC(C)(C)/C....
69 1YJ3 - MET C5 H11 N O2 S CSCC[C@@H]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: U19; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 U19 1 1
2 U12 0.4375 0.953488
3 U13 0.40678 0.886364
Similar Ligands (3D)
Ligand no: 1; Ligand: U19; Similar ligands found: 152
No: Ligand Similarity coefficient
1 ID8 0.9302
2 TLF 0.9183
3 LI4 0.9167
4 9RM 0.9151
5 DXK 0.9138
6 6J3 0.9122
7 AJD 0.9109
8 4GU 0.9082
9 1V1 0.9065
10 A73 0.9064
11 B23 0.9060
12 20D 0.9028
13 IKY 0.9020
14 DFL 0.9009
15 5E1 0.8997
16 AKD 0.8990
17 ELH 0.8981
18 6EN 0.8976
19 P9I 0.8961
20 3D8 0.8960
21 AUY 0.8953
22 QC1 0.8948
23 CJZ 0.8941
24 F40 0.8939
25 1FL 0.8939
26 DNQ 0.8932
27 MHB 0.8932
28 P4L 0.8931
29 BBY 0.8926
30 6TJ 0.8920
31 43S 0.8911
32 NKI 0.8897
33 25F 0.8896
34 9CE 0.8894
35 8HH 0.8891
36 7L4 0.8887
37 CZ0 0.8882
38 AQ1 0.8878
39 2GQ 0.8874
40 3Y7 0.8864
41 4F8 0.8858
42 JF8 0.8856
43 1V4 0.8855
44 SA0 0.8852
45 3B4 0.8851
46 BGC OXZ 0.8850
47 B21 0.8849
48 145 0.8846
49 DBQ 0.8845
50 WLH 0.8843
51 9OF 0.8841
52 BGC BGC 0.8839
53 7NU 0.8839
54 GAT 0.8838
55 M3W 0.8829
56 IFM BGC 0.8825
57 38E 0.8825
58 78Y 0.8824
59 RGK 0.8822
60 1BY 0.8822
61 X11 0.8820
62 5E2 0.8819
63 56N 0.8818
64 3GX 0.8811
65 8G6 0.8808
66 9MR 0.8806
67 WUB 0.8806
68 SZ5 0.8799
69 7ZL 0.8799
70 MBP 0.8797
71 1V3 0.8797
72 HMD 0.8795
73 IA2 0.8794
74 JRO 0.8788
75 5P3 0.8786
76 774 0.8778
77 CNI 0.8778
78 6BK 0.8771
79 IFM BMA 0.8770
80 A04 0.8770
81 EVO 0.8764
82 2AN 0.8758
83 3WK 0.8752
84 5NN 0.8742
85 CFK 0.8732
86 3F4 0.8728
87 5DN 0.8728
88 VT3 0.8722
89 IDZ 0.8713
90 2LX 0.8713
91 JNW 0.8713
92 HFT 0.8711
93 E9L 0.8709
94 BGC GAL 0.8707
95 ZRL 0.8702
96 GWD 0.8696
97 XYP XIF 0.8695
98 UKV 0.8691
99 JTA 0.8688
100 GNV 0.8682
101 C4E 0.8682
102 LUM 0.8680
103 H35 0.8677
104 II4 0.8665
105 CDJ 0.8654
106 CMU 0.8651
107 5AD 0.8651
108 IK1 0.8650
109 LR2 0.8649
110 NOY BGC 0.8648
111 ACE TRP 0.8647
112 XIF XYP 0.8645
113 0SY 0.8643
114 FCD 0.8643
115 GLC GAL 0.8638
116 W8L 0.8635
117 DDC 0.8630
118 LU2 0.8624
119 4E3 0.8624
120 ZRK 0.8621
121 NW1 0.8620
122 BGC Z9D 0.8618
123 9JT 0.8615
124 H2W 0.8611
125 2QU 0.8601
126 ISX 0.8600
127 CMG 0.8598
128 MNX 0.8592
129 57D 0.8588
130 JWS 0.8587
131 KCH 0.8578
132 F18 0.8578
133 NU3 0.8577
134 7D0 0.8575
135 5E5 0.8574
136 PA1 GCS 0.8573
137 MR6 0.8571
138 SHG BGC 0.8570
139 2D2 0.8564
140 9KQ 0.8564
141 YEX 0.8563
142 SQM 0.8560
143 NRA 0.8555
144 XDN XYP 0.8552
145 XYP XDN 0.8552
146 HA6 0.8551
147 B4L 0.8551
148 UL1 0.8550
149 XIL 0.8546
150 VAR 0.8541
151 XDL XYP 0.8537
152 MR4 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YVM; Ligand: TMG; 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: 1yvm.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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