Receptor
PDB id Resolution Class Description Source Keywords
3gvb 1.8 Å EC: 3.5.2.6 AMPC BETA-LACTAMASE IN COMPLEX WITH FRAGMENT-BASED INHIBITOR ESCHERICHIA COLI HYDROLASE 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
3GV A:1;
 Valid;
 none;
 Ki = 2.6 mM
221.209 C11 H11 N O4 c1ccc...
DMS A:365;
B:1;
B:362;
B:363;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
78.133 C2 H6 O S CS(=O...
PO4 A:3;
A:362;
A:363;
A:364;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
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: 3GV; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 3GV 1 1
2 GF7 0.4 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: 3GV; Similar ligands found: 110
No: Ligand Similarity coefficient
1 FCD 0.9512
2 WVV 0.9501
3 AUV 0.9437
4 YE6 0.9433
5 5C1 0.9416
6 9UL 0.9375
7 5F8 0.9373
8 5FL 0.9337
9 G14 0.9334
10 B21 0.9286
11 0LO 0.9281
12 X6P 0.9280
13 MD6 0.9275
14 1SF 0.9273
15 1ER 0.9249
16 EQA 0.9232
17 D1Y 0.9229
18 U2Z 0.9222
19 3TC 0.9207
20 D2G 0.9203
21 KYN 0.9202
22 3VW 0.9197
23 0NX 0.9193
24 XI7 0.9184
25 GXD 0.9183
26 3C5 0.9180
27 D1G 0.9172
28 TRP 0.9164
29 E9S 0.9163
30 6MW 0.9161
31 PUE 0.9081
32 4FF 0.9078
33 78Y 0.9049
34 GXG 0.9036
35 GZV 0.9028
36 7QS 0.9014
37 TT4 0.9009
38 LTT 0.8982
39 ETV 0.8977
40 1A7 0.8965
41 ENG 0.8958
42 7Q1 0.8957
43 D3G 0.8947
44 ZZZ 0.8938
45 BVS 0.8936
46 H35 0.8913
47 36M 0.8892
48 I2E 0.8889
49 NK5 0.8887
50 BZS 0.8868
51 YZM 0.8864
52 C53 0.8856
53 0OY 0.8843
54 7VP 0.8841
55 61M 0.8839
56 LDC 0.8836
57 27M 0.8805
58 PQT 0.8791
59 CK2 0.8789
60 S46 0.8789
61 LLT 0.8785
62 TOH 0.8783
63 P4F 0.8776
64 LTN 0.8776
65 LAH 0.8774
66 X6W 0.8774
67 848 0.8767
68 F63 0.8764
69 X11 0.8763
70 DBS 0.8756
71 A7K 0.8755
72 THU 0.8750
73 60L 0.8748
74 PA5 0.8747
75 78U 0.8747
76 CH8 0.8739
77 TQL 0.8737
78 EAJ 0.8726
79 2B4 0.8720
80 4Z9 0.8719
81 6J9 0.8710
82 BHS 0.8695
83 L13 0.8684
84 FPL 0.8683
85 5M2 0.8681
86 T2D 0.8680
87 ALA DGL 0.8670
88 56D 0.8667
89 ZEA 0.8664
90 SOV 0.8662
91 HJ7 0.8656
92 ZIQ 0.8651
93 CK1 0.8650
94 6J5 0.8648
95 EQW 0.8644
96 SIZ 0.8606
97 ALE 0.8602
98 BSA 0.8601
99 SV4 0.8593
100 RIS 0.8575
101 7QD 0.8570
102 DPN 0.8570
103 54F 0.8559
104 ZIP 0.8549
105 5LD 0.8544
106 5XW 0.8543
107 3IP 0.8542
108 OJD 0.8530
109 JRB 0.8528
110 2KU 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
APoc FAQ
Feedback