Receptor
PDB id Resolution Class Description Source Keywords
2GG2 1 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 METHIONINE 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:703;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
U12 A:801;
 Valid;
 none;
 ic50 = 0.25 uM
268.198 C10 H7 F3 N6 c1cc(...
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: U12; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 U12 1 1
2 U14 0.540984 0.765957
3 U13 0.465517 0.928571
4 U19 0.4375 0.953488
Similar Ligands (3D)
Ligand no: 1; Ligand: U12; Similar ligands found: 253
No: Ligand Similarity coefficient
1 T21 0.9625
2 Q2S 0.9406
3 801 0.9294
4 6FX 0.9277
5 6F3 0.9265
6 4RG 0.9245
7 NFL 0.9224
8 9RM 0.9215
9 MT6 0.9209
10 PJK 0.9193
11 7G2 0.9172
12 1V8 0.9159
13 IDZ 0.9147
14 JSX 0.9137
15 S1D 0.9125
16 BBP 0.9125
17 Q4G 0.9123
18 122 0.9123
19 E2N 0.9110
20 Z3R 0.9098
21 BMC 0.9073
22 MTB 0.9067
23 TVC 0.9067
24 WG8 0.9064
25 VBC 0.9061
26 Q92 0.9053
27 97K 0.9044
28 FLF 0.9029
29 6BK 0.9020
30 0DJ 0.9015
31 47V 0.9010
32 RGK 0.9005
33 B4L 0.9001
34 BMZ 0.8998
35 CR4 0.8995
36 108 0.8992
37 DFL 0.8980
38 L5D 0.8973
39 ESJ 0.8970
40 A45 0.8970
41 LU2 0.8969
42 B06 0.8969
43 20D 0.8969
44 1XS 0.8961
45 6TJ 0.8961
46 205 0.8954
47 120 0.8953
48 28A 0.8943
49 NZ4 0.8940
50 M83 0.8939
51 NKI 0.8935
52 GW9 0.8923
53 EEY 0.8919
54 IQQ 0.8919
55 LC1 0.8917
56 WLH 0.8914
57 FX5 0.8908
58 XEV 0.8908
59 08C 0.8908
60 2PW 0.8908
61 BXS 0.8907
62 AV7 0.8906
63 HHB 0.8902
64 VM7 0.8895
65 39R 0.8893
66 NU3 0.8873
67 C4E 0.8870
68 2QU 0.8869
69 0FS 0.8869
70 7FZ 0.8868
71 LZ7 0.8866
72 JCQ 0.8865
73 QR2 0.8864
74 9JT 0.8864
75 GAA 0.8863
76 121 0.8862
77 GLA BEZ 0.8861
78 TVZ 0.8861
79 D25 0.8860
80 H32 0.8857
81 1V1 0.8857
82 UV4 0.8857
83 A73 0.8856
84 3D8 0.8853
85 38E 0.8853
86 C0V 0.8852
87 0NJ 0.8851
88 5F8 0.8851
89 RF2 0.8850
90 JF5 0.8850
91 U4J 0.8849
92 X2M 0.8848
93 338 0.8846
94 AV4 0.8846
95 0UL 0.8842
96 124 0.8840
97 9CE 0.8839
98 F40 0.8838
99 LR2 0.8837
100 6JM 0.8837
101 AGI 0.8837
102 A63 0.8831
103 FSE 0.8829
104 IPJ 0.8828
105 5WK 0.8827
106 8M5 0.8825
107 EMU 0.8816
108 4AU 0.8816
109 SNJ 0.8816
110 4YE 0.8814
111 0LO 0.8812
112 OUA 0.8810
113 245 0.8809
114 28B 0.8806
115 6C8 0.8805
116 3Q0 0.8801
117 272 0.8797
118 V2Z 0.8797
119 27F 0.8795
120 IK1 0.8788
121 6DQ 0.8787
122 BZC 0.8782
123 SZ5 0.8782
124 3F4 0.8781
125 LI7 0.8780
126 QS4 0.8775
127 E9L 0.8774
128 G2V 0.8772
129 NFZ 0.8768
130 QUE 0.8765
131 RK4 0.8765
132 57D 0.8762
133 25F 0.8762
134 5KN 0.8759
135 CMG 0.8758
136 U98 0.8754
137 T34 0.8753
138 1V3 0.8752
139 581 0.8751
140 8KW 0.8751
141 NAR 0.8750
142 4ZF 0.8745
143 EFX 0.8745
144 M3W 0.8741
145 7L4 0.8740
146 ZEA 0.8740
147 W8L 0.8738
148 5TO 0.8738
149 L3L 0.8738
150 UN3 0.8735
151 CDJ 0.8734
152 5NN 0.8733
153 DFV 0.8733
154 4FF 0.8732
155 1UZ 0.8731
156 KWB 0.8731
157 H2W 0.8728
158 GQZ 0.8728
159 NIF 0.8727
160 1V4 0.8724
161 4GU 0.8722
162 PIQ 0.8720
163 QKU 0.8719
164 AVA 0.8717
165 1V0 0.8716
166 4YF 0.8716
167 2QV 0.8715
168 MR4 0.8712
169 88X 0.8710
170 1HP 0.8709
171 H6D 0.8705
172 3JC 0.8702
173 HKK 0.8701
174 4K2 0.8701
175 SSY 0.8700
176 II4 0.8698
177 DXK 0.8697
178 5E5 0.8695
179 5WW 0.8693
180 ZRK 0.8692
181 0MB 0.8686
182 HH6 0.8684
183 6QT 0.8683
184 4G2 0.8680
185 T61 0.8678
186 4L2 0.8676
187 JVB 0.8671
188 34L 0.8667
189 TH1 0.8667
190 OUG 0.8666
191 ZRL 0.8666
192 XYP XDN 0.8663
193 Q7U 0.8663
194 AQ1 0.8659
195 5B2 0.8659
196 1UT 0.8657
197 5R9 0.8656
198 0X2 0.8655
199 MYC 0.8655
200 P4L 0.8655
201 KWV 0.8655
202 DDC 0.8652
203 6JO 0.8649
204 VT3 0.8649
205 0SY 0.8649
206 SDT 0.8647
207 ISX 0.8646
208 1UR 0.8645
209 3WL 0.8642
210 NAB 0.8640
211 JBB 0.8638
212 6JP 0.8636
213 F18 0.8634
214 BRY 0.8634
215 1ER 0.8631
216 A0R 0.8630
217 FHV 0.8629
218 MR6 0.8628
219 WDW 0.8627
220 YIP 0.8626
221 IMK 0.8623
222 40N 0.8622
223 3Q1 0.8621
224 MHB 0.8620
225 X2L 0.8620
226 0K7 0.8619
227 69W 0.8617
228 5P3 0.8615
229 G30 0.8614
230 5P7 0.8610
231 H35 0.8607
232 SU9 0.8605
233 A05 0.8600
234 2D2 0.8594
235 8CC 0.8594
236 103 0.8592
237 T5J 0.8587
238 YE7 0.8584
239 0DF 0.8581
240 LIG 0.8577
241 XDN XYP 0.8576
242 E42 0.8575
243 QUG 0.8574
244 802 0.8573
245 T7O 0.8567
246 A64 0.8563
247 A6W 0.8559
248 BGC BGC 0.8557
249 IIH 0.8549
250 LJ5 0.8549
251 DN8 0.8548
252 5DE 0.8545
253 AVX 0.8515
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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