Receptor
PDB id Resolution Class Description Source Keywords
3gqz 1.8 Å EC: 3.5.2.6 AMPC BETA-LACTAMASE IN COMPLEX WITH FRAGMENT-BASED INHIBITOR ESCHERICHIA COLI HYDROLASE LACTAMASE FRAGMENT ANTIBIOTIC RESISTANCE PERIPLASM HYDROLASE/HYDROLASE INHIBITOR COMPLEX
Ref.: DOCKING FOR FRAGMENT INHIBITORS OF AMPC BETA-LACTAMASE 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
DMS A:1;
A:363;
 Invalid;
Invalid;
 none;
none;
 submit data
78.133 C2 H6 O S CS(=O...
GF7 A:362;
 Valid;
 none;
 Ki = 6.7 mM
247.247 C13 H13 N O4 CC(=O...
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: GF7; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GF7 1 1
2 SO7 0.4 0.689655
3 3GV 0.4 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: GF7; Similar ligands found: 162
No: Ligand Similarity coefficient
1 A05 0.9226
2 TVZ 0.9208
3 J1K 0.9199
4 A9B 0.9181
5 RYJ 0.9142
6 WLH 0.9111
7 NVS 0.9090
8 ESJ 0.9069
9 0K7 0.9061
10 20D 0.9061
11 TID 0.9060
12 4AU 0.9051
13 72G 0.9046
14 BX4 0.9045
15 1V8 0.9044
16 1XS 0.9043
17 HHB 0.9042
18 WDW 0.9038
19 NKI 0.9036
20 124 0.9032
21 IDZ 0.9029
22 SZ5 0.8990
23 LI7 0.8990
24 RGK 0.8989
25 5YA 0.8988
26 M5A 0.8985
27 4FC 0.8985
28 BRY 0.8978
29 4UM 0.8978
30 Q2S 0.8977
31 LWA 0.8970
32 272 0.8968
33 5M2 0.8967
34 O53 0.8959
35 U4J 0.8949
36 L2K 0.8948
37 25F 0.8942
38 RPN 0.8938
39 6T5 0.8934
40 8V8 0.8933
41 28A 0.8917
42 135 0.8915
43 42R 0.8913
44 1FL 0.8907
45 HH6 0.8906
46 3F4 0.8905
47 5TU 0.8899
48 N5B 0.8899
49 FMQ 0.8895
50 WF4 0.8887
51 T21 0.8885
52 WG8 0.8884
53 TVC 0.8877
54 0UL 0.8870
55 IXM 0.8859
56 6FX 0.8857
57 338 0.8854
58 C0V 0.8849
59 ARJ 0.8842
60 NOC 0.8842
61 5ZM 0.8840
62 90M 0.8840
63 XYP XYP 0.8832
64 VBC 0.8829
65 S1C 0.8827
66 3K1 0.8827
67 S1D 0.8821
68 J27 0.8818
69 SJR 0.8813
70 2UV 0.8810
71 6H2 0.8806
72 5WW 0.8801
73 4RG 0.8801
74 A8D 0.8788
75 5O6 0.8787
76 Q92 0.8786
77 6P3 0.8779
78 FBC 0.8779
79 1A5 0.8778
80 0MB 0.8778
81 1V4 0.8777
82 9JT 0.8776
83 3CA 0.8755
84 J84 0.8754
85 C4F 0.8753
86 JCQ 0.8752
87 3Q0 0.8752
88 121 0.8751
89 NAR 0.8750
90 GVI 0.8749
91 397 0.8749
92 BXS 0.8748
93 72H 0.8747
94 A9E 0.8745
95 KWV 0.8745
96 SNV 0.8741
97 FSE 0.8741
98 OSY 0.8738
99 90G 0.8734
100 BVS 0.8729
101 KU1 0.8728
102 JFS 0.8726
103 1HP 0.8725
104 H75 0.8721
105 ADN 0.8712
106 A18 0.8710
107 A4N 0.8709
108 1V3 0.8702
109 E9L 0.8701
110 22M 0.8697
111 NZ4 0.8696
112 5FD 0.8695
113 MTA 0.8693
114 UN9 0.8692
115 MI2 0.8692
116 OSP 0.8691
117 U55 0.8688
118 A5Q 0.8683
119 1OT 0.8683
120 613 0.8682
121 A45 0.8682
122 JPQ 0.8681
123 1R5 0.8679
124 CBE 0.8679
125 CDJ 0.8666
126 D1Y 0.8665
127 W8L 0.8664
128 6DQ 0.8649
129 XYS XYP 0.8648
130 0NJ 0.8646
131 XYS AZI XYS 0.8645
132 LR8 0.8638
133 2JX 0.8636
134 250 0.8633
135 TCL 0.8631
136 EF2 0.8630
137 UN3 0.8628
138 6F3 0.8624
139 M2E 0.8623
140 DCN 0.8621
141 5TO 0.8620
142 7G1 0.8616
143 RVE 0.8609
144 H2W 0.8607
145 ENG 0.8606
146 TH1 0.8606
147 DFV 0.8602
148 Y3J 0.8601
149 68C 0.8598
150 AD3 0.8598
151 3AD 0.8596
152 VIB 0.8581
153 GVO 0.8580
154 1E5 0.8576
155 FT3 0.8575
156 A4Q 0.8572
157 AX1 0.8572
158 1AJ 0.8566
159 6BK 0.8552
160 FY8 0.8551
161 N9M 0.8548
162 B7H 0.8514
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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