Receptor
PDB id Resolution Class Description Source Keywords
3G31 1.7 Å EC: 3.5.2.6 CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 4 (GF1) ESCHERICHIA COLI CTX-M BETA-LACTAMASE MOLECULAR DOCKING FRAGMENT INHIBITOR ANTIBIOTIC RESISTANCE HYDROLASE PLASMID HYDROLASE/HYDROLASE INHIBITOR COMPLEX
Ref.: MOLECULAR DOCKING AND LIGAND SPECIFICITY IN FRAGMENT-BASED INHIBITOR DISCOVERY NAT.CHEM.BIOL. V. 5 358 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS A:10;
A:9;
B:8;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
GF1 A:1;
A:2;
A:4;
B:3;
B:5;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Ki = 1.3 mM
237.252 C12 H15 N O4 C[C@@...
PO4 A:6;
B:7;
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
3G35 1.41 Å EC: 3.5.2.6 CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 12 (F13) ESCHERICHIA COLI CTX-M BETA-LACTAMASE MOLECULAR DOCKING FRAGMENT INHIBITOR ANTIBIOTIC RESISTANCE HYDROLASE PLASMID HYDROLASE/HYDROLASE INHIBITOR COMPLEX
Ref.: MOLECULAR DOCKING AND LIGAND SPECIFICITY IN FRAGMENT-BASED INHIBITOR DISCOVERY NAT.CHEM.BIOL. V. 5 358 2009
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
2 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
3 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
4 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
5 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
6 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
7 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
8 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
9 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
10 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
2 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
3 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
4 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
5 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
6 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
7 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
8 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
9 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
10 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
11 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
4 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
5 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
6 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
7 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
8 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
9 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
10 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
11 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
12 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
13 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
14 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
15 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
16 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
17 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
18 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
19 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
20 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
21 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
22 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
23 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
24 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
25 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
26 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
27 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
28 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
29 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
30 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
31 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
32 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GF1; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GF1 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3G35; Ligand: F13; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 3g35.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2RC8 DSN 0.006292 0.43626 1.52091
2 3HUN ZZ7 0.000002258 0.60203 1.90114
3 2RCA GLY 0.006876 0.43469 1.90114
4 1P7T PYR 0.008937 0.4313 2.28137
5 4P87 4NP 0.01206 0.42028 2.6616
6 1D8C GLV 0.007834 0.41828 2.6616
7 1NE7 16G 0.02941 0.40022 3.04183
8 1II7 DA 0.01804 0.41211 3.42205
9 3UEC ALA ARG TPO LYS 0.0004186 0.50133 3.42466
10 5HWK BEZ 0.02348 0.40177 3.75
11 4K79 GAL A2G 0.006814 0.43305 4.09091
12 4KQR VPP 0.00008553 0.48696 4.18251
13 1YQS BSA 0.0001146 0.40714 4.18251
14 3AI3 SOE 0.01468 0.41586 4.56274
15 2EFX NFA 0.02349 0.40645 4.56274
16 4OUE IPT 0.02582 0.40035 4.94297
17 4C2C ALA ALA ALA 0.02281 0.40374 5.70342
18 4RHS SIA SIA GAL 0.006452 0.41447 5.7377
19 3I5C C2E 0.02728 0.40324 5.82524
20 3I7V B4P 0.04937 0.40849 5.97015
21 3IHB GLU 0.001987 0.46767 7.22433
22 4J6O CIT 0.02946 0.40019 7.98479
23 1JOC ITP 0.001909 0.47495 8
24 4K91 SIN 0.00001038 0.59361 8.36502
25 2BVE PH5 0.03088 0.40692 8.40336
26 5X7Q GLC GLC 0.01234 0.40898 9.12547
27 3R75 BEZ 0.0241 0.40472 9.88593
28 2VGK REZ 0.001549 0.46902 10.2662
29 2IMG MLT 0.01352 0.41604 11.2583
Pocket No.: 2; Query (leader) PDB : 3G35; Ligand: F13; 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: 3g35.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3G35; Ligand: F13; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3g35.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3G35; Ligand: F13; Similar sites found: 5
This union binding pocket(no: 4) in the query (biounit: 3g35.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WQN ADP 0.01319 0.41177 2.6616
2 3WUR O4B 0.0298 0.40551 4.67836
3 4H69 10Y 0.01567 0.41198 5.15464
4 4KQP GLN 0.03207 0.40542 6.03448
5 4ZGM 32M 0.01982 0.4116 12.2951
Pocket No.: 5; Query (leader) PDB : 3G35; Ligand: F13; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3g35.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3G35; Ligand: F13; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3g35.bio2) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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