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 35 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 29 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 15 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: 25
This union binding pocket(no: 1) in the query (biounit: 1pi5.bio2) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4LOO SB4 0.01184 0.42042 1.95531
2 3HQP OXL 0.02741 0.41758 2.7933
3 4K91 SIN 0.007981 0.43166 2.89017
4 4EZW ASN ARG LEU LEU LEU THR GLY 0.0255 0.4074 3.19635
5 5DA3 58V 0.04913 0.40253 3.39623
6 4UAA 3GK 0.0002247 0.52514 3.42205
7 4UA7 3GK 0.0002255 0.52506 3.42205
8 1PVS 7HP 0.009836 0.44127 3.5461
9 2IW3 ADP 0.04433 0.40491 3.63128
10 2A9W GA9 0.03603 0.41728 4.16667
11 3LTW HLZ 0.03337 0.42071 4.28571
12 4KBA 1QM 0.03988 0.41096 5.43807
13 5N49 8LW 0.04178 0.41369 5.92593
14 3NZ1 3NY 0.03966 0.41371 6.13027
15 1YQC GLV 0.02298 0.43956 7.05882
16 5IGL BMF 0.04689 0.41163 7.09677
17 1PVC ILE SER GLU VAL 0.03909 0.40411 7.6412
18 3IT7 TLA 0.03061 0.40723 7.69231
19 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.02963 0.42043 7.85714
20 4I67 G G G RPC 0.03487 0.41046 9.1954
21 3AJ4 SEP 0.01557 0.42677 11.6071
22 1JOC ITP 0.01242 0.42908 12.8
23 3HUN ZZ7 0.003773 0.46609 14.8045
24 3HLF SIM 0.0003842 0.48271 21.5084
25 1YQS BSA 0.00004862 0.42648 31.2321
Pocket No.: 2; Query (leader) PDB : 1PI5; Ligand: SM2; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1PI5; Ligand: SM2; Similar sites found: 13
This union binding pocket(no: 3) in the query (biounit: 1pi5.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JY4 ISC 0.03715 0.40561 1.95531
2 1GT6 OLA 0.04937 0.40233 3.71747
3 3B6R CRN 0.03928 0.41014 3.91061
4 4PEG 5GP 0.04271 0.41762 4.18994
5 2PUZ NIG 0.04708 0.414 4.46927
6 3HEE R5P 0.04214 0.4129 4.69799
7 1GMN IDS SGN IDS SGN IDS 0.032 0.42832 4.91803
8 1M5W DXP 0.03781 0.41938 6.99588
9 3OEN GLU 0.02734 0.41939 7.69231
10 2Z48 NGA 0.03036 0.42616 7.82123
11 2Z49 AMG 0.02207 0.42466 7.82123
12 5TCI MLI 0.04724 0.41638 11.2319
13 1ZD9 GDP 0.01722 0.41294 13.2979
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