Receptor
PDB id Resolution Class Description Source Keywords
4DHY 2.38 Å EC: 2.7.1.2 CRYSTAL STRUCTURE OF HUMAN GLUCOKINASE IN COMPLEX WITH GLUCO ACTIVATOR HOMO SAPIENS DIABETES MELLITUS DISEASE MUTATION GLYCOLYSIS TRANSFERASETRANSFERASE-TRANSFERASE ACTIVATOR COMPLEX
Ref.: INSIGHTS INTO MECHANISM OF GLUCOKINASE ACTIVATION: OBSERVATION OF MULTIPLE DISTINCT PROTEIN CONFORMATI J.BIOL.CHEM. V. 287 13598 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLC A:501;
Valid;
none;
submit data
180.156 C6 H12 O6 C([C@...
NA A:503;
Part of Protein;
none;
submit data
22.99 Na [Na+]
S41 A:502;
Valid;
none;
submit data
432.432 C22 H20 N6 O4 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DHY 2.38 Å EC: 2.7.1.2 CRYSTAL STRUCTURE OF HUMAN GLUCOKINASE IN COMPLEX WITH GLUCO ACTIVATOR HOMO SAPIENS DIABETES MELLITUS DISEASE MUTATION GLYCOLYSIS TRANSFERASETRANSFERASE-TRANSFERASE ACTIVATOR COMPLEX
Ref.: INSIGHTS INTO MECHANISM OF GLUCOKINASE ACTIVATION: OBSERVATION OF MULTIPLE DISTINCT PROTEIN CONFORMATI J.BIOL.CHEM. V. 287 13598 2012
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3FGU - BGC C6 H12 O6 C([C@@H]1[....
2 3IDH - GLC C6 H12 O6 C([C@@H]1[....
3 3VEV - GLC C6 H12 O6 C([C@@H]1[....
4 5V4W - 8WM C21 H23 F N4 O4 S2 c1cc2c(cnn....
5 4ISE - 1FW C20 H21 F N4 O2 S c1cc2c(cc1....
6 3VF6 - GLC C6 H12 O6 C([C@@H]1[....
7 4DHY - S41 C22 H20 N6 O4 Cc1cc2c(o1....
8 4RCH - 3LZ C19 H19 N5 O2 S CCc1c(cccn....
9 3VEY - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
10 3IMX - GLC C6 H12 O6 C([C@@H]1[....
11 3A0I - GLC C6 H12 O6 C([C@@H]1[....
12 5V4X - 8WJ C22 H29 N3 O4 S2 c1csc(n1)N....
13 4ISF - GLC C6 H12 O6 C([C@@H]1[....
14 3F9M - MRK C14 H12 F N5 O S2 Cn1ccnc1Sc....
15 4DCH - GLC C6 H12 O6 C([C@@H]1[....
16 1V4S - MRK C14 H12 F N5 O S2 Cn1ccnc1Sc....
17 3H1V - TK1 C24 H20 N4 O5 S CS(=O)(=O)....
18 3ID8 - GLC C6 H12 O6 C([C@@H]1[....
19 3QIC - GLC C6 H12 O6 C([C@@H]1[....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3FGU - BGC C6 H12 O6 C([C@@H]1[....
2 3IDH - GLC C6 H12 O6 C([C@@H]1[....
3 3VEV - GLC C6 H12 O6 C([C@@H]1[....
4 5V4W - 8WM C21 H23 F N4 O4 S2 c1cc2c(cnn....
5 4ISE - 1FW C20 H21 F N4 O2 S c1cc2c(cc1....
6 3VF6 - GLC C6 H12 O6 C([C@@H]1[....
7 4DHY - S41 C22 H20 N6 O4 Cc1cc2c(o1....
8 4RCH - 3LZ C19 H19 N5 O2 S CCc1c(cccn....
9 3VEY - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
10 3IMX - GLC C6 H12 O6 C([C@@H]1[....
11 3A0I - GLC C6 H12 O6 C([C@@H]1[....
12 5V4X - 8WJ C22 H29 N3 O4 S2 c1csc(n1)N....
13 4ISF - GLC C6 H12 O6 C([C@@H]1[....
14 3F9M - MRK C14 H12 F N5 O S2 Cn1ccnc1Sc....
15 4DCH - GLC C6 H12 O6 C([C@@H]1[....
16 1V4S - MRK C14 H12 F N5 O S2 Cn1ccnc1Sc....
17 3H1V - TK1 C24 H20 N4 O5 S CS(=O)(=O)....
18 3ID8 - GLC C6 H12 O6 C([C@@H]1[....
19 3QIC - GLC C6 H12 O6 C([C@@H]1[....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3O5B - BGC C6 H12 O6 C([C@@H]1[....
2 3O80 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
3 3O8M - GLC C6 H12 O6 C([C@@H]1[....
4 3FGU - BGC C6 H12 O6 C([C@@H]1[....
5 3IDH - GLC C6 H12 O6 C([C@@H]1[....
6 3VEV - GLC C6 H12 O6 C([C@@H]1[....
7 5V4W - 8WM C21 H23 F N4 O4 S2 c1cc2c(cnn....
8 4ISE - 1FW C20 H21 F N4 O2 S c1cc2c(cc1....
9 3VF6 - GLC C6 H12 O6 C([C@@H]1[....
10 4DHY - S41 C22 H20 N6 O4 Cc1cc2c(o1....
11 4RCH - 3LZ C19 H19 N5 O2 S CCc1c(cccn....
12 3VEY - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
13 3IMX - GLC C6 H12 O6 C([C@@H]1[....
14 3A0I - GLC C6 H12 O6 C([C@@H]1[....
15 5V4X - 8WJ C22 H29 N3 O4 S2 c1csc(n1)N....
16 4ISF - GLC C6 H12 O6 C([C@@H]1[....
17 3F9M - MRK C14 H12 F N5 O S2 Cn1ccnc1Sc....
18 4DCH - GLC C6 H12 O6 C([C@@H]1[....
19 1V4S - MRK C14 H12 F N5 O S2 Cn1ccnc1Sc....
20 3H1V - TK1 C24 H20 N4 O5 S CS(=O)(=O)....
21 3ID8 - GLC C6 H12 O6 C([C@@H]1[....
22 3QIC - GLC C6 H12 O6 C([C@@H]1[....
23 4QS7 Kd = 89 uM BGC C6 H12 O6 C([C@@H]1[....
24 4QS9 Kd = 15 uM BGC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLC; Similar ligands found: 141
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL 1 1
2 BMA 1 1
3 GXL 1 1
4 GLA 1 1
5 ALL 1 1
6 GLC 1 1
7 BGC 1 1
8 GIV 1 1
9 MAN 1 1
10 WOO 1 1
11 32O 0.653846 0.866667
12 RIB 0.653846 0.866667
13 FUB 0.653846 0.866667
14 Z6J 0.653846 0.866667
15 AHR 0.653846 0.866667
16 BMA BMA MAN 0.545455 0.823529
17 GLA BGC 0.511628 0.848485
18 LAK 0.511628 0.848485
19 BGC GLA 0.511628 0.848485
20 GLA BMA 0.511628 0.848485
21 MAN BMA 0.511628 0.848485
22 GLA GLC 0.511628 0.848485
23 GAL GAL 0.511628 0.848485
24 MLB 0.511628 0.848485
25 BMA GLA 0.511628 0.848485
26 BMA BMA BMA BMA BMA BMA MAN 0.5 0.823529
27 YDR 0.5 0.8
28 MAN BMA BMA BMA BMA BMA 0.5 0.823529
29 GLC GLC GLC GLC BGC 0.488889 0.848485
30 GLC GLC GLC 0.488889 0.848485
31 MAN MAN MAN 0.488889 0.848485
32 GLC GLC GLC GLC GLC BGC 0.488889 0.848485
33 BGP 0.461538 0.675
34 G6P 0.461538 0.675
35 M6P 0.461538 0.675
36 A6P 0.461538 0.675
37 M6D 0.461538 0.675
38 BG6 0.461538 0.675
39 SHG 0.457143 0.875
40 GAF 0.457143 0.875
41 G2F 0.457143 0.875
42 X6X 0.457143 0.777778
43 2FG 0.457143 0.875
44 G3F 0.457143 0.875
45 PA1 0.457143 0.777778
46 1GN 0.457143 0.777778
47 GCS 0.457143 0.777778
48 2H5 0.457143 0.875
49 LB2 0.454545 0.848485
50 BGC BMA 0.454545 0.848485
51 BGC GAL 0.454545 0.848485
52 MAL 0.454545 0.848485
53 GLC GAL 0.454545 0.848485
54 M3M 0.454545 0.848485
55 GLA GAL 0.454545 0.848485
56 MAB 0.454545 0.848485
57 GLC BGC 0.454545 0.848485
58 BMA BMA 0.454545 0.848485
59 LBT 0.454545 0.848485
60 MAL MAL 0.454545 0.823529
61 CBK 0.454545 0.848485
62 GLA GLA 0.454545 0.848485
63 MAN GLC 0.454545 0.848485
64 CBI 0.454545 0.848485
65 N9S 0.454545 0.848485
66 GAL GLC 0.454545 0.848485
67 BMA GAL 0.454545 0.848485
68 B2G 0.454545 0.848485
69 BGC GLC 0.454545 0.848485
70 LAT 0.454545 0.848485
71 GAL BGC 0.454545 0.848485
72 3MG 0.444444 0.875
73 TCB 0.444444 0.8
74 GLC SGC 0.444444 0.8
75 YIO 0.441176 0.870968
76 2GS 0.432432 0.875
77 BGC BGC 0.431818 0.848485
78 2M4 0.431818 0.848485
79 MAN MAN 0.431818 0.848485
80 AHR AHR 0.428571 0.764706
81 GLF 0.428571 0.84375
82 FUB AHR 0.428571 0.764706
83 CT3 0.416667 0.848485
84 GLC BGC GLC 0.416667 0.848485
85 MLR 0.416667 0.848485
86 GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
87 GLC GLC GLC GLC GLC 0.416667 0.848485
88 GAL FUC 0.416667 0.848485
89 BMA BMA BMA 0.416667 0.848485
90 CTR 0.416667 0.848485
91 BGC GLC GLC 0.416667 0.848485
92 BGC GLC GLC GLC GLC 0.416667 0.848485
93 MAN MAN BMA BMA BMA BMA 0.416667 0.848485
94 GLC GAL GAL 0.416667 0.848485
95 B4G 0.416667 0.848485
96 CEX 0.416667 0.848485
97 MAN BMA BMA BMA BMA 0.416667 0.848485
98 BMA BMA BMA BMA BMA 0.416667 0.848485
99 GLC BGC BGC BGC BGC BGC 0.416667 0.848485
100 CTT 0.416667 0.848485
101 GLC GLC BGC 0.416667 0.848485
102 DXI 0.416667 0.848485
103 GLC GLC BGC GLC GLC GLC GLC 0.416667 0.848485
104 BGC GLC GLC GLC 0.416667 0.848485
105 BGC BGC BGC GLC 0.416667 0.848485
106 BGC BGC BGC BGC BGC BGC 0.416667 0.848485
107 BMA BMA BMA BMA BMA BMA 0.416667 0.848485
108 MTT 0.416667 0.848485
109 BMA MAN BMA 0.416667 0.848485
110 BGC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
111 CE5 0.416667 0.848485
112 GAL GAL GAL 0.416667 0.848485
113 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.848485
114 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
115 GLA GAL GLC 0.416667 0.848485
116 CE6 0.416667 0.848485
117 GLC BGC BGC BGC BGC 0.416667 0.848485
118 GLC BGC BGC 0.416667 0.848485
119 MAN BMA BMA 0.416667 0.848485
120 MT7 0.416667 0.848485
121 GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
122 CE8 0.416667 0.848485
123 CEY 0.416667 0.848485
124 BGC BGC BGC 0.408163 0.848485
125 BGC BGC BGC BGC BGC 0.408163 0.848485
126 GLC BGC BGC BGC BGC BGC BGC 0.408163 0.848485
127 SGC SGC BGC 0.408163 0.8
128 GLC BGC BGC BGC 0.408163 0.848485
129 BGC BGC BGC ASO BGC BGC ASO 0.408163 0.848485
130 BGC BGC BGC GLC BGC BGC 0.408163 0.848485
131 TRE 0.405405 0.848485
132 1LL 0.405405 0.771429
133 TDG 0.405405 0.771429
134 BM3 0.404762 0.7
135 NDG 0.404762 0.7
136 NAG 0.404762 0.7
137 HSQ 0.404762 0.7
138 A2G 0.404762 0.7
139 NGA 0.404762 0.7
140 FUB AHR AHR 0.4 0.764706
141 AHR AHR AHR 0.4 0.764706
Ligand no: 2; Ligand: S41; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S41 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DHY; Ligand: GLC; Similar sites found: 83
This union binding pocket(no: 1) in the query (biounit: 4dhy.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4M00 SUC 0.01566 0.40806 1.0661
2 5DNC ASN 0.02874 0.4076 1.70576
3 3ZJX BOG 0.01649 0.42503 1.7301
4 3WQT ANP 0.004669 0.417 2.1322
5 1SW1 PBE 0.04416 0.40226 2.18182
6 3WMX THR 0.02146 0.41359 2.23464
7 4B9Q ATP 0.00389 0.42044 2.34542
8 2DQA NAG NAG NAG 0.0268 0.40536 2.41935
9 1TUU AMP 0.001047 0.48223 2.50627
10 1TUU ADP 0.00426 0.45588 2.50627
11 1TUU PIS 0.001471 0.4548 2.50627
12 5W3Y IHP 0.02386 0.41184 2.55682
13 5W3Y ACO 0.04191 0.40682 2.55682
14 2ACV UDP 0.02445 0.40033 2.59179
15 1SQK ADP 0.0006884 0.47034 2.65252
16 2V51 ATP 0.0006393 0.45451 2.65252
17 4B1X ATP 0.0007189 0.45229 2.65957
18 4B1W ATP 0.0007662 0.44729 2.65957
19 4B1Y ATP 0.0008193 0.40236 2.65957
20 3MN9 ATP 0.0007971 0.4543 2.6738
21 3MN6 ATP 0.001114 0.44403 2.6738
22 2UYT ADP 0.000388 0.43557 2.77186
23 2UYT LRH 0.000388 0.43557 2.77186
24 2V7Y ADP 0.00459 0.42769 2.98507
25 3EFS BTN 0.01494 0.40082 3.00429
26 2A3Z ATP 0.00109 0.44829 3.07692
27 4ZWP M44 0.02267 0.41718 3.18182
28 5EOU ATP 0.00858 0.40549 3.22581
29 5BWD FUM 0.03462 0.40892 3.33333
30 2CH5 NAG 0.00428 0.44125 3.45821
31 2CH5 NDG 0.00502 0.43783 3.45821
32 3BF1 PAU 0.02237 0.40568 3.61446
33 2E2P ADP 0.0001062 0.5143 3.67893
34 2QXL ATP 0.001958 0.43702 4.05117
35 5L2R LMR 0.02797 0.40442 4.05117
36 1VJ7 GPX 0.01028 0.43093 4.58015
37 3UYW TAU 0.03993 0.40193 4.6729
38 4AQ0 DMJ 0.02016 0.41992 4.69083
39 4GNI ATP 0.00224 0.44619 4.90405
40 3CTL S6P 0.008609 0.4117 5.19481
41 3LL5 IP8 0.04357 0.40192 5.22088
42 4PL8 ATP 0.0006939 0.45697 5.47945
43 1FZQ GDP 0.0328 0.40088 5.52486
44 3SJH ATP 0.0008561 0.449 5.55556
45 4A2B AGS 0.005473 0.41399 5.72792
46 1KXP ATP 0.000867 0.45268 5.8952
47 4PKG ATP 0.0007821 0.45467 5.91398
48 4Z94 ATP 0.0007249 0.46468 6.13497
49 1Y7P RIP 0.02107 0.4066 6.27803
50 5HTX ADP 0.005596 0.4399 6.37813
51 2JBM SRT 0.01033 0.40705 6.68896
52 1P0Z FLC 0.01143 0.43448 6.87023
53 2FF3 ATP 0.0009285 0.45137 7.33333
54 1T44 ATP 0.001134 0.44753 7.48299
55 4EHU ANP 0.0006094 0.44781 7.6087
56 5W3X IHP 0.03015 0.40651 8.75
57 2D0O ADP 0.0007433 0.47361 8.8
58 1YAG ATP 0.0006979 0.40858 8.8
59 5F6U 5VK 0.02239 0.41412 8.9172
60 3MN7 ATP 0.0008706 0.44493 9.18367
61 3U4L ATP 0.001241 0.44201 9.28571
62 2PBD ATP 0.001297 0.44494 9.35252
63 5F7R GLC GLC 0.00003102 0.43595 9.40594
64 2BUP ADP 0.002768 0.42032 9.44882
65 2BUP ATP 0.002768 0.42032 9.44882
66 4YDU ADP 0.00332 0.42016 9.91254
67 4RW3 IPD 0.03827 0.40107 10.2649
68 2G77 AF3 0.0439 0.40242 11.1111
69 2QWO ADP 0.002768 0.42033 11.9565
70 1VBO MAN 0.0118 0.4373 12.0805
71 1VBO MAN MAN MAN 0.04134 0.40699 12.0805
72 4CBX ATP 0.0005499 0.46144 12.5984
73 4CBU ATP 0.001614 0.42687 12.5984
74 1WOQ BGC 0.0000231 0.56016 13.8577
75 2CJU PHX 0.04199 0.40171 15.9292
76 5LY3 ADP 0.01458 0.4013 18.75
77 3JUC PCA 0.0324 0.40794 19.6078
78 2D1K ATP 0.001421 0.44318 21.875
79 3MN5 ATP 0.0007685 0.40024 23.6842
80 4B1V ATP 0.00375 0.40097 25
81 2V52 ATP 0.0007848 0.40017 25
82 3U9Z ADP 0.0008804 0.46079 27.5862
83 2FF6 ATP 0.0007784 0.45476 42.3077
Pocket No.: 2; Query (leader) PDB : 4DHY; Ligand: S41; Similar sites found: 31
This union binding pocket(no: 2) in the query (biounit: 4dhy.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2D7I NGA 0.02905 0.40498 1.70576
2 4LH7 NMN 0.02666 0.4095 1.85759
3 5FQK 6NT 0.03893 0.40109 1.85874
4 3SHZ 5CO 0.02336 0.40189 2.01729
5 3X01 AMP 0.03585 0.40109 2.03562
6 2Z9I GLY ALA THR VAL 0.01413 0.4256 2.16049
7 5KBE IPH 0.01976 0.41378 2.18341
8 3TDC 0EU 0.0000005582 0.64667 2.55864
9 2Q4X HMH 0.02108 0.41307 2.71493
10 4LOC OXM 0.01288 0.40962 2.77186
11 2WPW ACO 0.01342 0.4027 2.94985
12 3RET SAL 0.01608 0.4025 2.9703
13 3RET PYR 0.01608 0.4025 2.9703
14 4G8R 96P 0.01164 0.42484 3.41151
15 4WQ2 3SU 0.01006 0.40504 3.46821
16 4TV1 36M 0.02754 0.4062 3.58566
17 2QE4 JJ3 0.01352 0.40727 3.62903
18 3R4S SIA 0.0005875 0.5017 4.28894
19 5BRP PNG 0.02538 0.40287 4.69083
20 5KJW 53C 0.0286 0.40612 5.62061
21 5LUN OGA 0.01005 0.42014 5.68182
22 1OW4 2AN 0.01158 0.41709 6.20155
23 1GEG GLC 0.02476 0.42137 6.25
24 4A69 I0P 0.03411 0.4013 6.38298
25 5AVF TAU 0.01191 0.42074 6.61479
26 5L2J 6UL 0.02833 0.40033 6.66667
27 4JX1 CAH 0.04552 0.40097 7.9646
28 5EE7 5MV 0.01092 0.42665 8.95522
29 3TL1 JRO 0.01504 0.42 9.43396
30 4RW3 SHV 0.008125 0.44394 10.2649
31 3KO0 TFP 0.01489 0.4229 20.7921
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