Receptor
PDB id Resolution Class Description Source Keywords
5K1D 1.94 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF A CLASS C BETA LACTAMASE/COMPOUND1 COMP ENTEROBACTER AEROGENES CLASS C BETA-LACTAMASE HYDROLASE
Ref.: GMP AND IMP ARE COMPETITIVE INHIBITORS OF CMY-10, A EXTENDED-SPECTRUM CLASS C BETA-LACTAMASE. ANTIMICROB. AGENTS V. 61 2017 CHEMOTHER.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:401;
Valid;
none;
Ki = 20.8 uM
363.221 C10 H14 N5 O8 P c1nc2...
CD A:403;
A:406;
A:402;
A:404;
A:405;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
112.411 Cd [Cd+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K1F 1.94 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF A CLASS C BETA LACTAMASE/COMPOUND2 COMP ENTEROBACTER AEROGENES CLASS C BETA-LACTAMASE HYDROLASE
Ref.: GMP AND IMP ARE COMPETITIVE INHIBITORS OF CMY-10, A EXTENDED-SPECTRUM CLASS C BETA-LACTAMASE. ANTIMICROB. AGENTS V. 61 2017 CHEMOTHER.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5K1F Ki = 16.2 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
2 5K1D Ki = 20.8 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 5K1F Ki = 16.2 uM IMP C10 H13 N4 O8 P c1nc2c(n1[....
2 5K1D Ki = 20.8 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
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: 5GP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K1F; Ligand: IMP; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 5k1f.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DCM SAM 0.02015 0.43542 1.04167
2 4UAA 3GK 0.000536 0.43211 1.90114
3 4UA7 3GK 0.0005973 0.43043 1.90114
4 4KQR VPP 0.01502 0.41382 2.18579
5 4K91 SIN 0.005276 0.40854 2.60116
6 5E7V M7E 0.03779 0.40517 5
7 2WYA HMG 0.02713 0.41587 5.19126
8 1PJS SAH 0.006288 0.43397 5.7377
9 3CYQ AMU 0.01545 0.40134 5.7971
10 3HUN ZZ7 0.001124 0.42831 7.37705
11 3I7V B4P 0.03185 0.41095 8.95522
12 4YNU FAD 0.04814 0.41288 12.8415
13 1YQS BSA 0.001582 0.48667 30.3725
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