Receptor
PDB id Resolution Class Description Source Keywords
6D15 1.3 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 1 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
TWB A:301;
A:302;
Valid;
Valid;
none;
none;
Ki = 32.9 uM
268.202 C12 H13 O5 P Cc1cc...
GOL A:303;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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: TWB; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 TWB 1 1
2 FUJ 0.551724 0.877551
3 VKE 0.551724 0.792453
4 GTV 0.459016 0.956522
5 YKG 0.421875 0.877551
6 XJE 0.415385 0.897959
7 P9T 0.412698 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: TWB; Similar ligands found: 129
No: Ligand Similarity coefficient
1 7SX 0.9527
2 KED 0.9471
3 EY7 0.9358
4 F95 0.9325
5 L8J 0.9318
6 2T4 0.9317
7 772 0.9278
8 T6Z 0.9250
9 M3Q 0.9220
10 8RK 0.9177
11 3E2 0.9161
12 JHY 0.9151
13 QMS 0.9148
14 H05 0.9140
15 A0O 0.9131
16 I59 0.9112
17 NPL 0.9102
18 AVR 0.9088
19 982 0.9085
20 AO6 0.9059
21 CLI 0.9053
22 GNR 0.9052
23 3N4 0.9043
24 GO1 0.9037
25 790 0.9036
26 EYM 0.9005
27 KWQ 0.9002
28 CX4 0.8998
29 9UG 0.8994
30 CSN 0.8977
31 EYA 0.8958
32 28S 0.8935
33 7ZC 0.8932
34 BN1 0.8916
35 NLA 0.8910
36 EV3 0.8903
37 FXH 0.8900
38 QVK 0.8896
39 7M2 0.8890
40 LF5 0.8889
41 CRZ 0.8887
42 96U 0.8879
43 7FF 0.8862
44 KWH 0.8858
45 MYI 0.8856
46 ALN 0.8843
47 APQ 0.8833
48 FWB 0.8832
49 5OF 0.8830
50 TQU 0.8816
51 JTF 0.8810
52 TDH 0.8809
53 IBM 0.8798
54 IOS 0.8791
55 S0I 0.8785
56 96R 0.8783
57 XM5 0.8780
58 NWD 0.8780
59 MRX 0.8763
60 LZB 0.8755
61 UMP 0.8748
62 DU 0.8748
63 8EQ 0.8741
64 S3P 0.8741
65 PLP 0.8739
66 GO0 0.8734
67 7M5 0.8734
68 WUB 0.8734
69 L07 0.8733
70 I6G 0.8732
71 8WZ 0.8723
72 JYT 0.8723
73 MS0 0.8719
74 B61 0.8718
75 VYM 0.8712
76 JAK 0.8712
77 AIR 0.8707
78 8GK 0.8707
79 0Q2 0.8702
80 7M6 0.8702
81 2J9 0.8701
82 6DP 0.8691
83 2SX 0.8688
84 JYK 0.8688
85 ZON 0.8683
86 EXL 0.8680
87 BB4 0.8677
88 SRO 0.8676
89 TXW 0.8674
90 LJW 0.8674
91 O83 0.8667
92 LP8 0.8667
93 JXK 0.8664
94 JUO 0.8662
95 ZO9 0.8659
96 OKM 0.8655
97 I46 0.8653
98 XG1 0.8652
99 67X 0.8649
100 C8O 0.8649
101 5PX 0.8645
102 8HG 0.8642
103 9LI 0.8642
104 29Q 0.8637
105 KOM 0.8632
106 SBK 0.8631
107 SNB 0.8629
108 K66 0.8625
109 ML2 0.8623
110 JY2 0.8623
111 4VS 0.8621
112 W22 0.8618
113 LQG 0.8617
114 F52 0.8613
115 1X8 0.8603
116 KFN 0.8602
117 YM6 0.8600
118 SG6 0.8599
119 PMP 0.8593
120 BK9 0.8587
121 JVE 0.8582
122 JXT 0.8581
123 3RH 0.8580
124 M5N 0.8578
125 1YE 0.8567
126 LEB 0.8554
127 96Z 0.8550
128 8DA 0.8538
129 GC2 0.8535
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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