Receptor
PDB id Resolution Class Description Source Keywords
6D18 1.35 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 6 KLEBSIELLA PNEUMONIAE BETA-LACTAMASE CARBAPENEMASE PHOSPHONATE INHIBITOR HYDROHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HETEROARYL PHOSPHONATES AS NONCOVALENT INHIBITORS O SERINE- AND METALLOCARBAPENEMASES. J.MED.CHEM. V. 62 8480 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:304;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
GTV A:303;
A:301;
A:302;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 1.4 uM
268.202 C12 H13 O5 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6D19 1.45 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 9 KLEBSIELLA PNEUMONIAE BETA-LACTAMASE CARBAPENEMASE PHOSPHONATE INHIBITOR HYDROHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HETEROARYL PHOSPHONATES AS NONCOVALENT INHIBITORS O SERINE- AND METALLOCARBAPENEMASES. J.MED.CHEM. V. 62 8480 2019
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 48 families.
1 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
2 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
3 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
4 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
5 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
6 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
7 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
8 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
9 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
10 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
11 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
12 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
13 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
14 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
2 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
3 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
4 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
5 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
6 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
7 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
8 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
9 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
10 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
11 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
12 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
13 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
14 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
4 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
5 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
6 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
7 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
8 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
9 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
10 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
11 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
12 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
13 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
14 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
15 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
16 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
17 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
18 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
19 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
20 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
21 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
22 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
23 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
24 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
25 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
26 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
27 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
28 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
29 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
30 6MIA - 1CE C12 H12 N6 O S C1CCc2c(c3....
31 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
32 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
33 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
34 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
35 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
36 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
37 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
38 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
39 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
40 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
41 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
42 6TY6 - 6NT C6 H4 N4 O2 c1cc2c(cc1....
43 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
44 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
45 6QW7 - DSN C3 H7 N O3 C([C@H](C(....
46 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
47 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
48 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
49 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
50 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
51 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
52 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
53 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
54 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
55 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
56 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
57 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GTV; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 GTV 1 1
2 YKG 0.62069 0.877551
3 XJE 0.610169 0.897959
4 P9T 0.508197 0.857143
5 TWB 0.459016 0.956522
6 7SX 0.444444 0.727273
7 FUJ 0.409091 0.877551
Similar Ligands (3D)
Ligand no: 1; Ligand: GTV; Similar ligands found: 115
No: Ligand Similarity coefficient
1 L8J 0.9713
2 KED 0.9386
3 F95 0.9369
4 VKE 0.9245
5 T6Z 0.9245
6 M3Q 0.9212
7 QMS 0.9158
8 790 0.9156
9 I59 0.9105
10 EY7 0.9101
11 LZB 0.9083
12 9LI 0.9080
13 H05 0.9072
14 CX4 0.9068
15 IBM 0.9067
16 CLI 0.9040
17 XM5 0.9034
18 8RK 0.9020
19 EV3 0.9009
20 GSY 0.9005
21 JHY 0.8965
22 ALN 0.8955
23 PLP 0.8943
24 EYM 0.8922
25 NLA 0.8919
26 9UG 0.8915
27 96R 0.8909
28 CRZ 0.8907
29 JYT 0.8905
30 GO0 0.8903
31 X04 0.8899
32 EYA 0.8892
33 JYK 0.8881
34 MS0 0.8877
35 JYW 0.8875
36 7M2 0.8865
37 5OF 0.8829
38 7FF 0.8826
39 96U 0.8821
40 GNR 0.8817
41 KWQ 0.8815
42 NPL 0.8809
43 IBC 0.8808
44 TRF 0.8801
45 FXH 0.8797
46 IOS 0.8796
47 PMP 0.8792
48 AVR 0.8791
49 SG6 0.8789
50 C8O 0.8786
51 982 0.8780
52 TXW 0.8770
53 8Y7 0.8767
54 LP8 0.8767
55 AO6 0.8754
56 3N4 0.8752
57 2N0 0.8734
58 B61 0.8728
59 G1P 0.8723
60 6DP 0.8719
61 67X 0.8718
62 JXZ 0.8710
63 FWB 0.8707
64 KZ9 0.8706
65 ST1 0.8705
66 96Z 0.8705
67 EXL 0.8703
68 KWH 0.8696
69 8HG 0.8695
70 7M6 0.8693
71 SBK 0.8692
72 XFE 0.8692
73 CSN 0.8692
74 GP1 0.8690
75 EGB 0.8688
76 2J9 0.8688
77 5PX 0.8663
78 AKD 0.8660
79 TQU 0.8656
80 K68 0.8656
81 OIA 0.8654
82 JXW 0.8648
83 MAG 0.8647
84 8GK 0.8644
85 LOG 0.8640
86 IOP 0.8637
87 AJD 0.8637
88 2LB 0.8633
89 E7R 0.8625
90 5WU 0.8622
91 A0O 0.8615
92 2J2 0.8614
93 TRP 0.8614
94 JUO 0.8614
95 Q9P 0.8614
96 IAC 0.8609
97 HHT 0.8606
98 ZON 0.8606
99 8DA 0.8604
100 GNT 0.8602
101 GO1 0.8595
102 39Z 0.8594
103 MP5 0.8592
104 0Q2 0.8585
105 7Z9 0.8584
106 W22 0.8583
107 XG1 0.8581
108 K66 0.8558
109 S0I 0.8550
110 3E2 0.8549
111 MUR 0.8543
112 L21 0.8538
113 DTR 0.8530
114 W8G 0.8516
115 54X 0.8502
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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