Receptor
PDB id Resolution Class Description Source Keywords
5IH1 1.31 Å EC: 2.-.-.- MACROLIDE 2'-PHOSPHOTRANSFERASE TYPE II - COMPLEX WITH GDP A PHOSPHORYLATED JOSAMYCIN ESCHERICHIA COLI MACROLIDE PHOSPHOTRANSFERASE KINASE TRANSFERASE
Ref.: STRUCTURAL BASIS FOR KINASE-MEDIATED MACROLIDE ANTI RESISTANCE. STRUCTURE V. 25 750 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6BQ A:404;
Valid;
none;
submit data
912.007 C42 H74 N O18 P C[C@@...
CA A:403;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
MG A:402;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
GDP A:401;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IH1 1.31 Å EC: 2.-.-.- MACROLIDE 2'-PHOSPHOTRANSFERASE TYPE II - COMPLEX WITH GDP A PHOSPHORYLATED JOSAMYCIN ESCHERICHIA COLI MACROLIDE PHOSPHOTRANSFERASE KINASE TRANSFERASE
Ref.: STRUCTURAL BASIS FOR KINASE-MEDIATED MACROLIDE ANTI RESISTANCE. STRUCTURE V. 25 750 2017
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 5IGY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5IGV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5IH1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 5IGZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5IGW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5IH0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 5IWU - ERY C37 H67 N O13 CC[C@@H]1[....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 5IGY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5IGV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5IH1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 5IGZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5IGW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5IH0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 5IWU - ERY C37 H67 N O13 CC[C@@H]1[....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 5IGY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5IGV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 5IH1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 5IGZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 5IGW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5IH0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 5IWU - ERY C37 H67 N O13 CC[C@@H]1[....
8 5IGT Kd = 0.2 uM ERY C37 H67 N O13 CC[C@@H]1[....
9 5IGI Kd = 0.17 uM ZIT C38 H72 N2 O12 CC[C@@H]1[....
10 5IGP Kd = 0.2 uM ERY C37 H67 N O13 CC[C@@H]1[....
11 5IGR - ZIO C35 H61 N O12 C[C@@H]1C[....
12 5IGS - GMP C10 H13 N5 O5 c1nc2c(n1[....
13 5IGJ Kd = 0.18 uM CTY C38 H69 N O13 CC[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6BQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 6BQ 1 1
Ligand no: 2; Ligand: GDP; Similar ligands found: 153
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IH1; Ligand: GDP; Similar sites found: 70
This union binding pocket(no: 1) in the query (biounit: 5ih1.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ZS4 ATP 0.01769 0.414 1.3245
2 4CUB GAL NAG 0.04652 0.415 1.63934
3 5UC9 MYR 0.03026 0.41506 1.76991
4 3V78 ET 0.02293 0.42137 1.92308
5 2PVF ACP 0.03848 0.40331 1.98676
6 5B25 4QJ 0.04892 0.40094 1.98676
7 1IA9 ANP 0.01475 0.41779 2.14286
8 3UIM ANP 0.009481 0.43031 2.31788
9 4CC6 L5Y 0.009726 0.4493 2.64901
10 4U98 ACP 0.009243 0.43436 2.98013
11 2WQN ADP 0.03048 0.41489 2.98013
12 2C91 TLA 0.04883 0.40819 2.98013
13 4BCN T9N 0.02084 0.42355 3.05344
14 4CFU 2WC 0.02851 0.41306 3.05344
15 2QES ADE 0.0114 0.45377 3.44828
16 1J1R ADE 0.04226 0.42049 3.44828
17 4V3I ASP LEU THR ARG PRO 0.0199 0.44215 3.50195
18 2YAK OSV 0.001159 0.44 3.50877
19 3PLS ANP 0.03221 0.40721 3.69128
20 1Y57 MPZ 0.003545 0.43722 3.97351
21 4R78 AMP 0.02602 0.42595 3.97351
22 3VMG 9CA 0.0323 0.41357 4.34783
23 4OCV ANP 0.0003651 0.49452 4.63576
24 5I35 ANP 0.002065 0.46672 4.63576
25 3IDB ANP 0.002779 0.44199 4.63576
26 4AG5 ADP 0.03433 0.4251 4.63576
27 3X01 AMP 0.03184 0.42464 4.63576
28 1XJD STU 0.02655 0.40549 4.63576
29 4WNP 3RJ 0.01153 0.43696 4.87805
30 3CY2 MB9 0.004057 0.43457 4.96689
31 4X7Q 3YR 0.01989 0.41455 4.96689
32 4BHN BH9 0.02745 0.40204 4.96689
33 2WDA L42 0.01693 0.44019 5.29801
34 5NCY 8TK 0.001379 0.43692 5.29801
35 3ORK AGS 0.00505 0.4244 5.62914
36 4IZY 1J2 0.007665 0.42816 5.96026
37 4UX9 ANP 0.009103 0.42465 5.96026
38 1OGX EQU 0.01781 0.42352 6.10687
39 4FFG LBS 0.01231 0.43703 6.62252
40 4FE2 ADP 0.02556 0.4189 6.66667
41 2R5T ANP 0.02407 0.40207 6.95364
42 1OJ4 CDM 0.04202 0.40754 7.42049
43 4BFM ANP 0.007971 0.42736 7.61589
44 2B9I ADP 0.03133 0.40484 8.60927
45 3KU0 ADE 0.03267 0.42867 8.76494
46 5LI9 ACP 0.01452 0.41812 8.9404
47 5EQY 5RA 0.0001341 0.43607 8.97756
48 2YW2 ATP 0.007593 0.42835 9.27152
49 1QCI ADE 0.01389 0.44533 9.54198
50 5IQD RIO 0.000002967 0.45351 9.60265
51 5IQD GNP 0.000003395 0.44859 9.60265
52 5DMZ ADP 0.02894 0.40654 9.60265
53 1TV5 N8E 0.004612 0.48611 10.2649
54 5OCA 9QZ 0.04731 0.42181 10.9244
55 1YRO UDP 0.005648 0.47195 11.3821
56 1LFO OLA 0.03063 0.40249 11.7188
57 1YC4 43P 0.01297 0.4343 11.7424
58 2A19 ANP 0.005058 0.46 13.7143
59 3W0O HY0 0.000003873 0.54096 13.9073
60 3W0O ADP 0.000003873 0.54096 13.9073
61 5LPZ ADP 0.01414 0.42182 13.9073
62 1U59 STU 0.01482 0.42082 22.2997
63 1M6P M6P 0.02899 0.42742 22.3684
64 4DFU QUE 0.0001078 0.56265 22.6708
65 4DFU KAN 0.01591 0.43764 22.6708
66 5C4L SIS 0.00001264 0.41771 22.7414
67 5C4L 4XR 0.00002204 0.41035 22.7414
68 3TM0 ANP 0.0002039 0.4643 25.0951
69 3TM0 B31 0.0002389 0.45853 25.0951
70 3TDV GDP 0.00000449 0.59204 28.8079
Pocket No.: 2; Query (leader) PDB : 5IH1; Ligand: 6BQ; Similar sites found: 72
This union binding pocket(no: 2) in the query (biounit: 5ih1.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ZS4 ATP 0.01769 0.414 1.3245
2 4CUB GAL NAG 0.04652 0.415 1.63934
3 4ANW O92 0.003025 0.41798 1.65563
4 5UC9 MYR 0.03026 0.41506 1.76991
5 3V78 ET 0.0219 0.42242 1.92308
6 2PVF ACP 0.04048 0.40219 1.98676
7 5B25 4QJ 0.04892 0.40094 1.98676
8 1IA9 ANP 0.01475 0.41779 2.14286
9 3UIM ANP 0.009481 0.43031 2.31788
10 4CC6 L5Y 0.009726 0.4493 2.64901
11 4U98 ACP 0.009206 0.43444 2.98013
12 2WQN ADP 0.03048 0.41489 2.98013
13 2C91 TLA 0.04883 0.40819 2.98013
14 4BCN T9N 0.02084 0.42355 3.05344
15 4CFU 2WC 0.02851 0.41306 3.05344
16 2QES ADE 0.0114 0.45377 3.44828
17 1J1R ADE 0.04226 0.42049 3.44828
18 4V3I ASP LEU THR ARG PRO 0.0199 0.44215 3.50195
19 2YAK OSV 0.002344 0.42752 3.50877
20 3PLS ANP 0.03375 0.40618 3.69128
21 1Y57 MPZ 0.003545 0.43722 3.97351
22 4R78 AMP 0.03908 0.41622 3.97351
23 1A78 TDG 0.02205 0.44044 4.47761
24 4OCV ANP 0.0006834 0.48153 4.63576
25 5I35 ANP 0.002065 0.46672 4.63576
26 3IDB ANP 0.002779 0.44199 4.63576
27 3X01 AMP 0.03184 0.42464 4.63576
28 4AG5 ADP 0.04012 0.42133 4.63576
29 1XJD STU 0.0286 0.40393 4.63576
30 4WNP 3RJ 0.008838 0.44297 4.87805
31 3CY2 MB9 0.004658 0.43186 4.96689
32 4X7Q 3YR 0.02393 0.41061 4.96689
33 4BHN BH9 0.02745 0.40204 4.96689
34 2WDA L42 0.01693 0.44019 5.29801
35 5NCY 8TK 0.001461 0.43589 5.29801
36 3ORK AGS 0.00505 0.4244 5.62914
37 5X8I SQZ 0.0459 0.40238 5.62914
38 4IZY 1J2 0.007665 0.42816 5.96026
39 4UX9 ANP 0.0112 0.42042 5.96026
40 1OGX EQU 0.01905 0.42203 6.10687
41 4FFG LBS 0.01231 0.43703 6.62252
42 4FE2 ADP 0.02721 0.41748 6.66667
43 2R5T ANP 0.02407 0.40207 6.95364
44 1OJ4 CDM 0.04356 0.40671 7.42049
45 4BFM ANP 0.007971 0.42736 7.61589
46 2B9I ADP 0.03738 0.40105 8.60927
47 3KU0 ADE 0.03267 0.42867 8.76494
48 5LI9 ACP 0.01653 0.41541 8.9404
49 5EQY 5RA 0.00006962 0.44544 8.97756
50 2YW2 ATP 0.007593 0.42835 9.27152
51 1QCI ADE 0.03393 0.41591 9.54198
52 5IQD RIO 0.000004777 0.44748 9.60265
53 5IQD GNP 0.000005294 0.44236 9.60265
54 5DMZ ADP 0.03148 0.40474 9.60265
55 1TV5 N8E 0.004612 0.48611 10.2649
56 5OCA 9QZ 0.04731 0.42181 10.9244
57 1YRO UDP 0.005648 0.47195 11.3821
58 1LFO OLA 0.03003 0.40291 11.7188
59 1YC4 43P 0.01297 0.4343 11.7424
60 2A19 ANP 0.005058 0.46 13.7143
61 3W0O ADP 0.00001709 0.51467 13.9073
62 3W0O HY0 0.00001709 0.51467 13.9073
63 5LPZ ADP 0.01497 0.42061 13.9073
64 1U59 STU 0.01497 0.42061 22.2997
65 1M6P M6P 0.02899 0.42742 22.3684
66 4DFU QUE 0.0001115 0.56184 22.6708
67 4DFU KAN 0.01591 0.43764 22.6708
68 5C4L SIS 0.00001264 0.41771 22.7414
69 5C4L 4XR 0.00002254 0.41002 22.7414
70 3TM0 ANP 0.000221 0.46292 25.0951
71 3TM0 B31 0.0002589 0.45717 25.0951
72 3TDV GDP 0.00000449 0.59204 28.8079
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