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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:2;
B:3;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
PO4 A:1;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
SM2 A:401;
B:400;
B:401;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 17 nM
319.141 C14 H14 B N O5 S B([C@...
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 (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 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 4KZB Ki = 1.3 mM NZ3 C10 H13 N O4 S C[C@H](C(=....
24 1L0G - SUC C12 H22 O11 C([C@@H]1[....
25 1MY8 Ki = 0.035 uM SM3 C13 H14 B N O3 S B([C@H](c1....
26 2HDS Ki = 10 mM 4MB C8 H9 N O4 S CS(=O)(=O)....
27 4OKP - 2V0 C8 H12 N2 O4 S CC1=C(N[C@....
28 3GRJ Ki = 1 mM G14 C10 H8 N2 O2 c1ccc(cc1)....
29 4KZ5 Ki < 10 mM 1U3 C13 H11 Cl N2 O4 Cc1c(c(no1....
30 3GVB Ki = 2.6 mM 3GV C11 H11 N O4 c1ccc(c(c1....
31 4KZ9 - 1U7 C15 H21 N O c1ccc(cc1)....
32 3GR2 Ki = 3 mM GF4 C7 H10 N6 O CCC1=C(NN(....
33 3GSG Ki = 2 mM GF1 C12 H15 N O4 C[C@@H](C(....
34 4JXV Ki = 31 uM 1MU C14 H13 N O6 S2 c1cc(ccc1C....
35 2HDQ Ki = 40 mM C21 C5 H4 O2 S c1cc(sc1)C....
36 4KZ6 Ki = 0.8 mM ZB6 C10 H17 N O3 S C[C@@H]1CC....
37 3GQZ Ki = 6.7 mM GF7 C13 H13 N O4 CC(=O)c1cc....
38 5JOC - CIT C6 H8 O7 C(C(=O)O)C....
39 4KZA Ki = 0.2 mM NZ9 C8 H9 N O4 S2 c1csc(c1S(....
70% Homology Family (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 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 4KZB Ki = 1.3 mM NZ3 C10 H13 N O4 S C[C@H](C(=....
24 1L0G - SUC C12 H22 O11 C([C@@H]1[....
25 1MY8 Ki = 0.035 uM SM3 C13 H14 B N O3 S B([C@H](c1....
26 2HDS Ki = 10 mM 4MB C8 H9 N O4 S CS(=O)(=O)....
27 4OKP - 2V0 C8 H12 N2 O4 S CC1=C(N[C@....
28 3GRJ Ki = 1 mM G14 C10 H8 N2 O2 c1ccc(cc1)....
29 4KZ5 Ki < 10 mM 1U3 C13 H11 Cl N2 O4 Cc1c(c(no1....
30 3GVB Ki = 2.6 mM 3GV C11 H11 N O4 c1ccc(c(c1....
31 4KZ9 - 1U7 C15 H21 N O c1ccc(cc1)....
32 3GR2 Ki = 3 mM GF4 C7 H10 N6 O CCC1=C(NN(....
33 3GSG Ki = 2 mM GF1 C12 H15 N O4 C[C@@H](C(....
34 4JXV Ki = 31 uM 1MU C14 H13 N O6 S2 c1cc(ccc1C....
35 2HDQ Ki = 40 mM C21 C5 H4 O2 S c1cc(sc1)C....
36 4KZ6 Ki = 0.8 mM ZB6 C10 H17 N O3 S C[C@@H]1CC....
37 3GQZ Ki = 6.7 mM GF7 C13 H13 N O4 CC(=O)c1cc....
38 5JOC - CIT C6 H8 O7 C(C(=O)O)C....
39 4KZA Ki = 0.2 mM NZ9 C8 H9 N O4 S2 c1csc(c1S(....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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 4KZB Ki = 1.3 mM NZ3 C10 H13 N O4 S C[C@H](C(=....
24 1L0G - SUC C12 H22 O11 C([C@@H]1[....
25 1MY8 Ki = 0.035 uM SM3 C13 H14 B N O3 S B([C@H](c1....
26 2HDS Ki = 10 mM 4MB C8 H9 N O4 S CS(=O)(=O)....
27 4OKP - 2V0 C8 H12 N2 O4 S CC1=C(N[C@....
28 3GRJ Ki = 1 mM G14 C10 H8 N2 O2 c1ccc(cc1)....
29 4KZ5 Ki < 10 mM 1U3 C13 H11 Cl N2 O4 Cc1c(c(no1....
30 3GVB Ki = 2.6 mM 3GV C11 H11 N O4 c1ccc(c(c1....
31 4KZ9 - 1U7 C15 H21 N O c1ccc(cc1)....
32 3GR2 Ki = 3 mM GF4 C7 H10 N6 O CCC1=C(NN(....
33 3GSG Ki = 2 mM GF1 C12 H15 N O4 C[C@@H](C(....
34 4JXV Ki = 31 uM 1MU C14 H13 N O6 S2 c1cc(ccc1C....
35 2HDQ Ki = 40 mM C21 C5 H4 O2 S c1cc(sc1)C....
36 4KZ6 Ki = 0.8 mM ZB6 C10 H17 N O3 S C[C@@H]1CC....
37 3GQZ Ki = 6.7 mM GF7 C13 H13 N O4 CC(=O)c1cc....
38 5JOC - CIT C6 H8 O7 C(C(=O)O)C....
39 4KZA Ki = 0.2 mM NZ9 C8 H9 N O4 S2 c1csc(c1S(....
40 5K1F Ki = 16.2 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
41 5K1D Ki = 20.8 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SM2; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 SM2 1 1
2 SM3 0.615385 0.906977
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: 42
This union binding pocket(no: 1) in the query (biounit: 1pi5.bio2) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 4WG0 CHD None
3 1SDW IYT 1.91083
4 1GPM AMP 2.51397
5 4K91 SIN 2.89017
6 4RF7 ARG 3.07263
7 1V6A TRE 3.31325
8 3IHB GLU 3.35196
9 4UAA 3GK 3.42205
10 4UA7 3GK 3.42205
11 1PVS 7HP 3.5461
12 3R6K FUC GAL GLA 3.60656
13 2IW3 ADP 3.63128
14 3EYK EYK 4.06977
15 3UEC ALA ARG TPO LYS 4.10959
16 2A9W GA9 4.16667
17 3LTW HLZ 4.28571
18 3HEE R5P 4.69799
19 6E1Q CFA 5.02793
20 4KBA 1QM 5.43807
21 2UVO NAG 5.84795
22 4LHD GLY 5.86592
23 3NZ1 3NY 6.13027
24 4FF8 14S 7.12074
25 4KQR VPP 7.26257
26 2Z3U CRR 7.26257
27 1PVC ILE SER GLU VAL 7.6412
28 4E28 0MZ 7.69231
29 3IT7 TLA 7.69231
30 2Z49 AMG 7.82123
31 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 7.85714
32 5KK4 44E 8.33333
33 5LX9 OLB 8.79479
34 5U5G 7VD 11.1864
35 3AJ4 SEP 11.6071
36 1JOC ITP 12.8
37 3HUN ZZ7 14.8045
38 4AP9 1PS 15.9204
39 3HLF SIM 21.5084
40 4P87 4NP 22.6257
41 2EFX NFA 25.1397
42 1YQS BSA 31.2321
Pocket No.: 2; Query (leader) PDB : 1PI5; Ligand: SM2; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 1pi5.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 4IYO NAK 1.39665
2 5IN3 G1P 2.51397
3 1HV6 MAW MAV GCU 2.5641
4 3W6X HZP 2.62009
5 1ZGS XMM 3.63128
6 4PEG 5GP 4.18994
7 2YP9 SIA CMO 4.18994
8 5X30 HCS 4.46927
9 5TSU CYS 4.7486
10 2J0W ASP 5.34521
11 3WW2 SF9 5.85938
12 5UFF 8B7 6.01852
13 2J73 GLC GLC GLC 7.76699
14 2Z48 NGA 7.82123
15 2Z48 A2G 7.82123
16 1VMK GUN 8.66426
17 5WAN URA 10.6145
18 5YRM BGC GLC 21.1268
19 3IWD M2T 27.4194
Pocket No.: 3; Query (leader) PDB : 1PI5; Ligand: SM2; Similar sites found with APoc: 16
This union binding pocket(no: 3) in the query (biounit: 1pi5.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 5A04 BGC 2.0649
2 3K6V CIT 2.25989
3 4RUS NAG 2.52101
4 5MLJ 9ST 2.67857
5 4XFM THE 2.7933
6 2WBV SIA 3.1746
7 4EZW ASN ARG LEU LEU LEU THR GLY 3.19635
8 4TVD BGC 3.63128
9 1GT6 OLA 3.71747
10 3B6R CRN 3.91061
11 5U75 SIA GAL NDG FUC 4.16667
12 2PUZ NIG 4.46927
13 6GH9 MIX 5.02793
14 5TCI MLI 11.2319
15 1ONI BEZ 12.3188
16 1ZD9 GDP 13.2979
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