Receptor
PDB id Resolution Class Description Source Keywords
3GTC 1.9 Å EC: 3.5.2.6 AMPC BETA-LACTAMASE IN COMPLEX WITH FRAGMENT-BASED INHIBITOR ESCHERICHIA COLI HYDROLASE ANTIBIOTIC RESISTANCE PERIPLASM HYDROLASE-HYDROINHIBITOR COMPLEX
Ref.: DOCKING FOR FRAGMENT INHIBITORS OF AMPC BETA-LACTAM PROC.NATL.ACAD.SCI.USA V. 106 7455 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTC A:362;
A:364;
B:1;
B:362;
B:363;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Ki = 4.5 mM
227.283 C9 H13 N3 O2 S C1CC[...
PO4 A:1;
A:363;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1PI5 1.49 Å EC: 3.5.2.6 STRUCTURE OF N289A MUTANT OF AMPC IN COMPLEX WITH SM2, CARBOXYPHENYLGLYCYLBORONIC ACID BEARING THE CEPHALOTHIN R1 S IDE CHAIN ESCHERICHIA COLI CRYSTAL STRUCTURE ENZYME INHIBITOR COMPLEX BETA-LACTAMASEHYDROLASE
Ref.: THERMODYNAMIC CYCLE ANALYSIS AND INHIBITOR DESIGN AGAINST BETA-LACTAMASE. BIOCHEMISTRY V. 42 14483 2003
Members (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 48 families.
1 1L2S Ki = 26 uM STC C11 H8 Cl N O4 S2 c1cc(ccc1N....
2 4OLD - 2UZ C7 H10 N2 O4 S C1C=C(NC(S....
3 4JXW Ki = 19 uM 1MW C15 H15 N O6 S2 c1cc(ccc1C....
4 4KZ8 Ki = 1.6 mM 1U6 C8 H12 N2 O2 S CCN1C(=O)C....
5 2HDU Ki = 5 mM F12 C7 H7 N O3 S CC(=O)Nc1c....
6 1KVL - KCP C14 H16 N2 O5 S2 CC1=C(N[C@....
7 1PI5 Ki = 17 nM SM2 C14 H14 B N O5 S B([C@H](c1....
8 2R9W Ki = 8 uM 23C C22 H15 N O6 c1ccc2c(c1....
9 2PU2 Ki = 37 uM DK2 C18 H13 N O7 c1cc(ccc1C....
10 1XGJ Ki = 1 uM HTC C12 H9 N O7 S2 c1cc(c(cc1....
11 1PI4 Ki = 37 nM SM3 C13 H14 B N O3 S B([C@H](c1....
12 1XGI Ki = 14 uM NST C11 H8 N2 O6 S2 c1cc(cc(c1....
13 3GV9 Ki = 7.5 mM GV9 C7 H7 N O3 S CC(=O)Nc1c....
14 1O07 - MXG C24 H36 N6 O9 S C[C@@H](C(....
15 3GTC Ki = 4.5 mM GTC C9 H13 N3 O2 S C1CC[C@H](....
16 4KZ3 Ki = 1.7 mM 1U1 C5 H4 Cl N O4 S2 c1c(c(sc1C....
17 4KZ7 Ki = 3.2 mM 1U5 C10 H14 O4 C[C@]12CC[....
18 2HDR Ki = 19 mM 4A3 C7 H7 N O3 c1cc(c(cc1....
19 1LL9 - AXL C16 H21 N3 O5 S CC1([C@@H]....
20 4JXS Ki = 18 uM 18U C13 H11 N O6 S2 c1cc(ccc1C....
21 2R9X Ki = 14 uM WH6 C23 H17 N O6 c1ccc2c(c1....
22 4KZ4 Ki = 0.07 mM 4A1 C10 H13 N O4 S CCCS(=O)(=....
23 6T5Y ic50 = 7.6 uM C8V C13 H23 N5 O7 S C1C[C@H](C....
24 4KZB Ki = 1.3 mM NZ3 C10 H13 N O4 S C[C@H](C(=....
25 1L0G - GLC FRU n/a n/a
26 1MY8 Ki = 0.035 uM SM3 C13 H14 B N O3 S B([C@H](c1....
27 2HDS Ki = 10 mM 4MB C8 H9 N O4 S CS(=O)(=O)....
28 4OKP - 2V0 C8 H12 N2 O4 S CC1=C(N[C@....
29 3GRJ Ki = 1 mM G14 C10 H8 N2 O2 c1ccc(cc1)....
30 4KZ5 Ki < 10 mM 1U3 C13 H11 Cl N2 O4 Cc1c(c(no1....
31 3GVB Ki = 2.6 mM 3GV C11 H11 N O4 c1ccc(c(c1....
32 4KZ9 - 1U7 C15 H21 N O c1ccc(cc1)....
33 3GR2 Ki = 3 mM GF4 C7 H10 N6 O CCC1=C(NN(....
34 3GSG Ki = 2 mM GF1 C12 H15 N O4 C[C@@H](C(....
35 6TPM ic50 = 6.61 uM MK7 C12 H22 N4 O6 S C1C[C@H](N....
36 4JXV Ki = 31 uM 1MU C14 H13 N O6 S2 c1cc(ccc1C....
37 2HDQ Ki = 40 mM C21 C5 H4 O2 S c1cc(sc1)C....
38 4KZ6 Ki = 0.8 mM ZB6 C10 H17 N O3 S C[C@@H]1CC....
39 3GQZ Ki = 6.7 mM GF7 C13 H13 N O4 CC(=O)c1cc....
40 5JOC - CIT C6 H8 O7 C(C(=O)O)C....
41 4KZA Ki = 0.2 mM NZ9 C8 H9 N O4 S2 c1csc(c1S(....
70% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 1L2S Ki = 26 uM STC C11 H8 Cl N O4 S2 c1cc(ccc1N....
2 4OLD - 2UZ C7 H10 N2 O4 S C1C=C(NC(S....
3 4JXW Ki = 19 uM 1MW C15 H15 N O6 S2 c1cc(ccc1C....
4 4KZ8 Ki = 1.6 mM 1U6 C8 H12 N2 O2 S CCN1C(=O)C....
5 2HDU Ki = 5 mM F12 C7 H7 N O3 S CC(=O)Nc1c....
6 1KVL - KCP C14 H16 N2 O5 S2 CC1=C(N[C@....
7 1PI5 Ki = 17 nM SM2 C14 H14 B N O5 S B([C@H](c1....
8 2R9W Ki = 8 uM 23C C22 H15 N O6 c1ccc2c(c1....
9 2PU2 Ki = 37 uM DK2 C18 H13 N O7 c1cc(ccc1C....
10 1XGJ Ki = 1 uM HTC C12 H9 N O7 S2 c1cc(c(cc1....
11 1PI4 Ki = 37 nM SM3 C13 H14 B N O3 S B([C@H](c1....
12 1XGI Ki = 14 uM NST C11 H8 N2 O6 S2 c1cc(cc(c1....
13 3GV9 Ki = 7.5 mM GV9 C7 H7 N O3 S CC(=O)Nc1c....
14 1O07 - MXG C24 H36 N6 O9 S C[C@@H](C(....
15 3GTC Ki = 4.5 mM GTC C9 H13 N3 O2 S C1CC[C@H](....
16 4KZ3 Ki = 1.7 mM 1U1 C5 H4 Cl N O4 S2 c1c(c(sc1C....
17 4KZ7 Ki = 3.2 mM 1U5 C10 H14 O4 C[C@]12CC[....
18 2HDR Ki = 19 mM 4A3 C7 H7 N O3 c1cc(c(cc1....
19 1LL9 - AXL C16 H21 N3 O5 S CC1([C@@H]....
20 4JXS Ki = 18 uM 18U C13 H11 N O6 S2 c1cc(ccc1C....
21 2R9X Ki = 14 uM WH6 C23 H17 N O6 c1ccc2c(c1....
22 4KZ4 Ki = 0.07 mM 4A1 C10 H13 N O4 S CCCS(=O)(=....
23 6T5Y ic50 = 7.6 uM C8V C13 H23 N5 O7 S C1C[C@H](C....
24 4KZB Ki = 1.3 mM NZ3 C10 H13 N O4 S C[C@H](C(=....
25 1L0G - GLC FRU n/a n/a
26 1MY8 Ki = 0.035 uM SM3 C13 H14 B N O3 S B([C@H](c1....
27 2HDS Ki = 10 mM 4MB C8 H9 N O4 S CS(=O)(=O)....
28 4OKP - 2V0 C8 H12 N2 O4 S CC1=C(N[C@....
29 3GRJ Ki = 1 mM G14 C10 H8 N2 O2 c1ccc(cc1)....
30 4KZ5 Ki < 10 mM 1U3 C13 H11 Cl N2 O4 Cc1c(c(no1....
31 3GVB Ki = 2.6 mM 3GV C11 H11 N O4 c1ccc(c(c1....
32 4KZ9 - 1U7 C15 H21 N O c1ccc(cc1)....
33 3GR2 Ki = 3 mM GF4 C7 H10 N6 O CCC1=C(NN(....
34 3GSG Ki = 2 mM GF1 C12 H15 N O4 C[C@@H](C(....
35 6TPM ic50 = 6.61 uM MK7 C12 H22 N4 O6 S C1C[C@H](N....
36 4JXV Ki = 31 uM 1MU C14 H13 N O6 S2 c1cc(ccc1C....
37 2HDQ Ki = 40 mM C21 C5 H4 O2 S c1cc(sc1)C....
38 4KZ6 Ki = 0.8 mM ZB6 C10 H17 N O3 S C[C@@H]1CC....
39 3GQZ Ki = 6.7 mM GF7 C13 H13 N O4 CC(=O)c1cc....
40 5JOC - CIT C6 H8 O7 C(C(=O)O)C....
41 4KZA Ki = 0.2 mM NZ9 C8 H9 N O4 S2 c1csc(c1S(....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 1L2S Ki = 26 uM STC C11 H8 Cl N O4 S2 c1cc(ccc1N....
2 4OLD - 2UZ C7 H10 N2 O4 S C1C=C(NC(S....
3 4JXW Ki = 19 uM 1MW C15 H15 N O6 S2 c1cc(ccc1C....
4 4KZ8 Ki = 1.6 mM 1U6 C8 H12 N2 O2 S CCN1C(=O)C....
5 2HDU Ki = 5 mM F12 C7 H7 N O3 S CC(=O)Nc1c....
6 1KVL - KCP C14 H16 N2 O5 S2 CC1=C(N[C@....
7 1PI5 Ki = 17 nM SM2 C14 H14 B N O5 S B([C@H](c1....
8 2R9W Ki = 8 uM 23C C22 H15 N O6 c1ccc2c(c1....
9 2PU2 Ki = 37 uM DK2 C18 H13 N O7 c1cc(ccc1C....
10 1XGJ Ki = 1 uM HTC C12 H9 N O7 S2 c1cc(c(cc1....
11 1PI4 Ki = 37 nM SM3 C13 H14 B N O3 S B([C@H](c1....
12 1XGI Ki = 14 uM NST C11 H8 N2 O6 S2 c1cc(cc(c1....
13 3GV9 Ki = 7.5 mM GV9 C7 H7 N O3 S CC(=O)Nc1c....
14 1O07 - MXG C24 H36 N6 O9 S C[C@@H](C(....
15 3GTC Ki = 4.5 mM GTC C9 H13 N3 O2 S C1CC[C@H](....
16 4KZ3 Ki = 1.7 mM 1U1 C5 H4 Cl N O4 S2 c1c(c(sc1C....
17 4KZ7 Ki = 3.2 mM 1U5 C10 H14 O4 C[C@]12CC[....
18 2HDR Ki = 19 mM 4A3 C7 H7 N O3 c1cc(c(cc1....
19 1LL9 - AXL C16 H21 N3 O5 S CC1([C@@H]....
20 4JXS Ki = 18 uM 18U C13 H11 N O6 S2 c1cc(ccc1C....
21 2R9X Ki = 14 uM WH6 C23 H17 N O6 c1ccc2c(c1....
22 4KZ4 Ki = 0.07 mM 4A1 C10 H13 N O4 S CCCS(=O)(=....
23 6T5Y ic50 = 7.6 uM C8V C13 H23 N5 O7 S C1C[C@H](C....
24 4KZB Ki = 1.3 mM NZ3 C10 H13 N O4 S C[C@H](C(=....
25 1L0G - GLC FRU n/a n/a
26 1MY8 Ki = 0.035 uM SM3 C13 H14 B N O3 S B([C@H](c1....
27 2HDS Ki = 10 mM 4MB C8 H9 N O4 S CS(=O)(=O)....
28 4OKP - 2V0 C8 H12 N2 O4 S CC1=C(N[C@....
29 3GRJ Ki = 1 mM G14 C10 H8 N2 O2 c1ccc(cc1)....
30 4KZ5 Ki < 10 mM 1U3 C13 H11 Cl N2 O4 Cc1c(c(no1....
31 3GVB Ki = 2.6 mM 3GV C11 H11 N O4 c1ccc(c(c1....
32 4KZ9 - 1U7 C15 H21 N O c1ccc(cc1)....
33 3GR2 Ki = 3 mM GF4 C7 H10 N6 O CCC1=C(NN(....
34 3GSG Ki = 2 mM GF1 C12 H15 N O4 C[C@@H](C(....
35 6TPM ic50 = 6.61 uM MK7 C12 H22 N4 O6 S C1C[C@H](N....
36 4JXV Ki = 31 uM 1MU C14 H13 N O6 S2 c1cc(ccc1C....
37 2HDQ Ki = 40 mM C21 C5 H4 O2 S c1cc(sc1)C....
38 4KZ6 Ki = 0.8 mM ZB6 C10 H17 N O3 S C[C@@H]1CC....
39 3GQZ Ki = 6.7 mM GF7 C13 H13 N O4 CC(=O)c1cc....
40 5JOC - CIT C6 H8 O7 C(C(=O)O)C....
41 4KZA Ki = 0.2 mM NZ9 C8 H9 N O4 S2 c1csc(c1S(....
42 6PWM - GLY C2 H5 N O2 C(C(=O)O)N
43 6PWL - GLY C2 H5 N O2 C(C(=O)O)N
44 6KA5 - 1S7 C15 H16 N2 O5 S2 CO[C@@](C=....
45 5K1F Ki = 16.2 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
46 5K1D Ki = 20.8 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GTC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GTC 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: GTC; Similar ligands found: 180
No: Ligand Similarity coefficient
1 AIN 0.9201
2 S3B 0.9167
3 60Q 0.9163
4 61O 0.9129
5 DNB 0.9106
6 M72 0.9073
7 B2Y 0.9062
8 52C 0.9042
9 FLC 0.9032
10 HA7 0.9032
11 F69 0.9029
12 87L 0.9024
13 B5D 0.9021
14 BZS 0.9013
15 2CZ 0.8996
16 AVI 0.8985
17 PRZ 0.8973
18 SQP 0.8972
19 LT8 0.8969
20 HHT 0.8965
21 Z5P 0.8958
22 BPS 0.8941
23 AVJ 0.8939
24 MCO 0.8934
25 SKM 0.8932
26 97T 0.8927
27 MOK 0.8926
28 URC 0.8922
29 QM1 0.8921
30 6XI 0.8917
31 AP4 0.8910
32 J9Q 0.8909
33 NZ2 0.8908
34 SR4 0.8907
35 CCB 0.8901
36 ZOL 0.8898
37 PH2 0.8894
38 CIT 0.8891
39 49N 0.8890
40 49O 0.8886
41 N2Z 0.8885
42 OBP 0.8881
43 CTN 0.8878
44 TH4 0.8873
45 1A7 0.8871
46 GLY ASP 0.8871
47 7UZ 0.8868
48 T2D 0.8861
49 NZ3 0.8859
50 QX4 0.8857
51 S2T 0.8856
52 Q71 0.8855
53 U2Z 0.8854
54 XQB 0.8849
55 KJM 0.8839
56 QIC 0.8822
57 QBS 0.8820
58 3CR 0.8819
59 1WC 0.8815
60 DQU 0.8810
61 CH9 0.8809
62 HHR 0.8806
63 NDH 0.8804
64 DHK 0.8802
65 8WO 0.8798
66 NI9 0.8798
67 ONR 0.8796
68 MPK 0.8796
69 ICT 0.8796
70 20J 0.8791
71 V6F 0.8791
72 FDR 0.8788
73 0GY 0.8782
74 7QS 0.8782
75 OCZ 0.8782
76 4V6 0.8776
77 256 0.8776
78 289 0.8772
79 TWO 0.8771
80 7Q1 0.8771
81 0F9 0.8769
82 AVO 0.8766
83 CTL 0.8766
84 B62 0.8764
85 PJW 0.8761
86 BPY 0.8761
87 GL4 0.8761
88 4ME 0.8756
89 44V 0.8755
90 RIS 0.8746
91 WOE 0.8745
92 2BQ 0.8744
93 XQK 0.8743
94 KYA 0.8741
95 44W 0.8740
96 NCD 0.8739
97 XHP 0.8737
98 091 0.8732
99 KDO 0.8728
100 DHZ 0.8727
101 ZB6 0.8724
102 HJ7 0.8724
103 2F6 0.8721
104 CK2 0.8713
105 APG 0.8713
106 8MO 0.8711
107 DNA 0.8709
108 787 0.8707
109 NCT 0.8706
110 SER THR 0.8706
111 UFO 0.8703
112 5VL 0.8703
113 F6P 0.8701
114 Q77 0.8698
115 JAA 0.8690
116 GLS 0.8686
117 GDE 0.8683
118 46P 0.8676
119 TRC 0.8676
120 4P0 0.8674
121 A7K 0.8664
122 791 0.8664
123 JF2 0.8664
124 GLY PRO 0.8662
125 TT4 0.8661
126 0UT 0.8660
127 9UL 0.8656
128 8NX 0.8655
129 ALA PRO 0.8653
130 6ME 0.8653
131 ACE PHE 0.8653
132 C9E 0.8650
133 F34 0.8648
134 GBN 0.8646
135 2AL 0.8644
136 JRB 0.8643
137 OMD 0.8634
138 5VJ 0.8633
139 URI 0.8632
140 ESI 0.8631
141 SQ7 0.8631
142 HHS 0.8630
143 9X5 0.8629
144 6W6 0.8629
145 2C0 0.8625
146 NSG 0.8623
147 293 0.8621
148 VNL 0.8620
149 9PL 0.8620
150 89J 0.8619
151 QQQ 0.8614
152 A9O 0.8614
153 GNL 0.8610
154 CP6 0.8607
155 8WT 0.8596
156 K2Q 0.8595
157 BCK 0.8589
158 H5B 0.8588
159 MIF 0.8586
160 X11 0.8585
161 ASC 0.8584
162 5XR 0.8577
163 6E8 0.8574
164 MN9 0.8572
165 CLU 0.8571
166 DUR 0.8568
167 1Z8 0.8568
168 1AL 0.8567
169 DX3 0.8567
170 AMQ 0.8566
171 JTH 0.8557
172 7A3 0.8554
173 KG1 0.8552
174 GC3 0.8539
175 KTW 0.8528
176 3Y7 0.8528
177 9FQ 0.8527
178 S2P 0.8521
179 DYT 0.8516
180 75K 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1PI5; Ligand: SM2; 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: 1pi5.bio2) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1PI5; Ligand: SM2; 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: 1pi5.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1PI5; Ligand: SM2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1pi5.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
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