Receptor
PDB id Resolution Class Description Source Keywords
4LY9 2.35 Å EC: 2.-.-.- HUMAN GKRP COMPLEXED TO AMG-1694 [(2R)-1,1,1-TRIFLUORO-2-{4- {[(3S)-3-METHYLMORPHOLIN-4-YL]METHYL}-4-(THIOPHEN-2-YLSULFOP IPERAZIN-1-YL]PHENYL}PROPAN-2-OL] AND SORBITOL-6-PHOSPHATE HOMO SAPIENS REGULATORY PROTEIN DISRUPTOR LIGAND COMPLEX SIS DOMAINS GTO GK LIVER CARBOHYDRATE BINDING PROTEIN
Ref.: ANTIDIABETIC EFFECTS OF GLUCOKINASE REGULATORY PROT SMALL-MOLECULE DISRUPTORS. NATURE V. 504 437 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IOD B:707;
B:710;
A:702;
B:701;
A:705;
A:711;
B:713;
B:711;
A:701;
A:708;
B:705;
A:703;
A:710;
B:714;
A:706;
B:706;
A:712;
A:704;
B:702;
B:712;
B:703;
B:709;
A:709;
A:707;
B:704;
B:708;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
126.904 I [I-]
SO4 B:718;
B:719;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
1YY A:714;
B:716;
Valid;
Valid;
none;
none;
Kd = 0.007 uM
533.627 C23 H30 F3 N3 O4 S2 C[C@H...
S6P A:713;
B:715;
Valid;
Valid;
none;
none;
submit data
262.152 C6 H15 O9 P C([C@...
GOL B:717;
A:715;
Invalid;
Invalid;
none;
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
4LY9 2.35 Å EC: 2.-.-.- HUMAN GKRP COMPLEXED TO AMG-1694 [(2R)-1,1,1-TRIFLUORO-2-{4- {[(3S)-3-METHYLMORPHOLIN-4-YL]METHYL}-4-(THIOPHEN-2-YLSULFOP IPERAZIN-1-YL]PHENYL}PROPAN-2-OL] AND SORBITOL-6-PHOSPHATE HOMO SAPIENS REGULATORY PROTEIN DISRUPTOR LIGAND COMPLEX SIS DOMAINS GTO GK LIVER CARBOHYDRATE BINDING PROTEIN
Ref.: ANTIDIABETIC EFFECTS OF GLUCOKINASE REGULATORY PROT SMALL-MOLECULE DISRUPTORS. NATURE V. 504 437 2013
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 4MQU - S6P C6 H15 O9 P C([C@@H]([....
2 4LY9 Kd = 0.007 uM 1YY C23 H30 F3 N3 O4 S2 C[C@H]1COC....
3 4OLH - S6P C6 H15 O9 P C([C@@H]([....
4 4OHP - S6P C6 H15 O9 P C([C@@H]([....
5 4MSU ic50 = 1.42 uM 2EU C17 H16 F6 N2 O3 S2 c1cc(sc1)S....
6 4OHM - S6P C6 H15 O9 P C([C@@H]([....
7 4MRO - MG0 C18 H18 F6 N4 O3 S c1cc(ccc1C....
8 4BB9 - F1P C6 H13 O9 P C1[C@H]([C....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 4MQU - S6P C6 H15 O9 P C([C@@H]([....
2 4LY9 Kd = 0.007 uM 1YY C23 H30 F3 N3 O4 S2 C[C@H]1COC....
3 4OLH - S6P C6 H15 O9 P C([C@@H]([....
4 4OHP - S6P C6 H15 O9 P C([C@@H]([....
5 4MSU ic50 = 1.42 uM 2EU C17 H16 F6 N2 O3 S2 c1cc(sc1)S....
6 4OHM - S6P C6 H15 O9 P C([C@@H]([....
7 4MRO - MG0 C18 H18 F6 N4 O3 S c1cc(ccc1C....
8 4BB9 - F1P C6 H13 O9 P C1[C@H]([C....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 4MQU - S6P C6 H15 O9 P C([C@@H]([....
2 4LY9 Kd = 0.007 uM 1YY C23 H30 F3 N3 O4 S2 C[C@H]1COC....
3 4OLH - S6P C6 H15 O9 P C([C@@H]([....
4 4OHP - S6P C6 H15 O9 P C([C@@H]([....
5 4MSU ic50 = 1.42 uM 2EU C17 H16 F6 N2 O3 S2 c1cc(sc1)S....
6 4OHM - S6P C6 H15 O9 P C([C@@H]([....
7 4MRO - MG0 C18 H18 F6 N4 O3 S c1cc(ccc1C....
8 4BB9 - F1P C6 H13 O9 P C1[C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1YY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1YY 1 1
Ligand no: 2; Ligand: S6P; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 S6P 1 1
2 M2P 0.821429 0.941176
3 DX5 0.71875 0.970588
4 A5P 0.71875 0.970588
5 LXP 0.71875 0.970588
6 M6R 0.621622 0.804878
7 G6Q 0.621622 0.885714
8 AGP 0.621622 0.804878
9 LX1 0.571429 0.885714
10 6PG 0.564103 0.861111
11 LG6 0.564103 0.861111
12 KD0 0.560976 0.861111
13 I22 0.536585 0.942857
14 H4P 0.534884 0.785714
15 HG3 0.53125 0.852941
16 DG6 0.526316 0.942857
17 R5P 0.526316 0.885714
18 R52 0.526316 0.885714
19 TX4 0.526316 0.673913
20 R10 0.512821 0.861111
21 PA5 0.512821 0.861111
22 PAI 0.489362 0.727273
23 TG6 0.487805 0.942857
24 F6R 0.487805 0.942857
25 1NT 0.479167 0.861111
26 1GP 0.470588 0.939394
27 G3P 0.470588 0.939394
28 LRY 0.468085 0.688889
29 2FP 0.465116 0.914286
30 P6T 0.465116 0.914286
31 PAN 0.465116 0.645833
32 P6F 0.465116 0.914286
33 MTL 0.464286 0.636364
34 SOR 0.464286 0.636364
35 E4P 0.459459 0.828571
36 5SP 0.439024 0.916667
37 HMS 0.439024 0.916667
38 5RP 0.439024 0.916667
39 DER 0.435897 0.861111
40 DEZ 0.435897 0.861111
41 52L 0.434783 0.659574
42 DXP 0.425 0.783784
43 4TP 0.414634 0.72093
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LY9; Ligand: S6P; Similar sites found: 38
This union binding pocket(no: 1) in the query (biounit: 4ly9.bio2) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ZS4 ATP 0.02933 0.40105 1.62866
2 5IXK 6EW 0.006014 0.40354 2.63158
3 5LX9 OLB 0.02882 0.41046 3.25733
4 5DCH 1YO 0.02352 0.43164 3.64583
5 5V4R MGT 0.0271 0.44206 3.7037
6 1N71 COA 0.02322 0.4031 3.88889
7 1TMX HGX 0.008427 0.4206 4.09556
8 5K53 STE 0.004078 0.43834 4.58015
9 3JUT GTQ 0.02449 0.41918 4.61538
10 5EW0 3C7 0.04839 0.41255 4.70085
11 4DK7 0KS 0.01022 0.4229 4.8583
12 5FUS DAO 0.03879 0.40706 4.87805
13 5DXE EST 0.002597 0.4633 4.98084
14 4UCC ZKW 0.01766 0.44528 5.02355
15 5F74 AMP 0.03989 0.41728 5.28455
16 5K04 COA 0.01221 0.41043 5.29412
17 3E3U NVC 0.03418 0.40667 5.58376
18 5K7H IVC 0.02052 0.40288 5.62771
19 4ZNO SUC 0.04456 0.41542 5.67164
20 4QVX 3CQ 0.01197 0.41657 5.98802
21 5UFS 1TA 0.01562 0.40561 6.45161
22 2YJD YJD 0.007375 0.43666 6.66667
23 5CMK LY5 0.01884 0.41984 6.94981
24 3RY9 1CA 0.01993 0.4121 7.6
25 4WGF HX2 0.047 0.41005 7.80488
26 1U3R 338 0.003364 0.44955 7.88382
27 4HBM 0Y7 0.03382 0.40381 8.33333
28 4UA3 COA 0.004697 0.43549 9.27835
29 5HCV 60R 0.01755 0.4088 10.1167
30 5ICK FEZ 0.01344 0.41724 10.917
31 5UNJ RJW 0.02433 0.41095 11.0204
32 1YRX FMN 0.03332 0.40413 13.2231
33 5LWY OLA 0.01364 0.41693 13.4454
34 5LWY OLB 0.02992 0.40963 13.4454
35 5F7Y GLC GAL NAG GAL FUC A2G 0.01254 0.43257 14.1667
36 5TWO 7MV 0.02687 0.40011 15.4412
37 5OCA 9QZ 0.0007561 0.53539 15.5462
38 4LZJ 22H 0.0000001725 0.44366 36.9637
Pocket No.: 2; Query (leader) PDB : 4LY9; Ligand: 1YY; Similar sites found: 41
This union binding pocket(no: 2) in the query (biounit: 4ly9.bio2) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AEE NSQ 0.03989 0.401 0.941915
2 4ZS4 ATP 0.02308 0.40685 1.62866
3 5IXK 6EW 0.0052 0.40692 2.63158
4 5LX9 OLB 0.02988 0.41046 3.25733
5 1QY8 RDI 0.04038 0.40073 3.34572
6 5DCH 1YO 0.0243 0.43164 3.64583
7 5V4R MGT 0.02791 0.44206 3.7037
8 1N71 COA 0.02416 0.4031 3.88889
9 1TMX HGX 0.008804 0.4206 4.09556
10 5K53 STE 0.004266 0.43834 4.58015
11 3JUT GTQ 0.02516 0.41918 4.61538
12 5LJI FMN 0.03195 0.40584 4.72973
13 4DK7 0KS 0.01065 0.4229 4.8583
14 5FUS DAO 0.04015 0.40706 4.87805
15 5DXE EST 0.003154 0.45998 4.98084
16 4UCC ZKW 0.0167 0.44697 5.02355
17 5F74 AMP 0.04057 0.41765 5.28455
18 5K04 COA 0.01275 0.41043 5.29412
19 3E3U NVC 0.03542 0.40667 5.58376
20 5K7H IVC 0.01911 0.40513 5.62771
21 4ZNO SUC 0.0458 0.41542 5.67164
22 4QVX 3CQ 0.01241 0.41669 5.98802
23 5UFS 1TA 0.01552 0.40656 6.45161
24 2YJD YJD 0.007682 0.43666 6.66667
25 5CMK LY5 0.01956 0.41984 6.94981
26 3RY9 1CA 0.02071 0.4121 7.6
27 4WGF HX2 0.04835 0.41005 7.80488
28 1U3R 338 0.003648 0.44876 7.88382
29 4HBM 0Y7 0.007409 0.43744 8.33333
30 4UA3 COA 0.004911 0.43549 9.27835
31 4WT2 3UD 0.01103 0.40061 9.52381
32 5HCV 60R 0.01828 0.4088 10.1167
33 5ICK FEZ 0.01339 0.41817 10.917
34 5UNJ RJW 0.02526 0.41095 11.0204
35 1YRX FMN 0.03456 0.40413 13.2231
36 5LWY OLA 0.01421 0.41693 13.4454
37 5LWY OLB 0.02953 0.41071 13.4454
38 5F7Y GLC GAL NAG GAL FUC A2G 0.01302 0.43257 14.1667
39 5TWO 7MV 0.0133 0.41527 15.4412
40 5OCA 9QZ 0.000784 0.53539 15.5462
41 4LZJ 22H 0.0000001865 0.43842 36.9637
Pocket No.: 3; Query (leader) PDB : 4LY9; Ligand: 1YY; Similar sites found: 17
This union binding pocket(no: 3) in the query (biounit: 4ly9.bio1) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NSA BEN 0.03925 0.41443 1.26582
2 4WOE 3S5 0.002523 0.46148 2.1978
3 3SQP 3J8 0.006002 0.46749 2.30126
4 4RW3 SHV 0.04445 0.43131 2.31788
5 4L9I 8PR 0.007004 0.44119 2.38095
6 5K9B FMN 0.02958 0.40397 2.77778
7 4OAS 2SW 0.01164 0.42351 3.125
8 5LOL GSH 0.02323 0.42611 3.25581
9 1JS8 MAN MAN BMA 0.04653 0.40611 4.82234
10 2C04 GCP 0.02914 0.40715 4.86656
11 5F2T PLM 0.02045 0.4179 4.87013
12 3JUC PCA 0.04237 0.42543 5.22876
13 5DKK FMN 0.02355 0.40596 5.51724
14 5VRH OLB 0.025 0.43489 5.55556
15 4X1Z FUC GAL NDG 0.03843 0.40867 7.53012
16 5EK3 5PK 0.0226 0.43008 9.67742
17 3G5K BB2 0.04861 0.40181 13.6612
Pocket No.: 4; Query (leader) PDB : 4LY9; Ligand: S6P; Similar sites found: 18
This union binding pocket(no: 4) in the query (biounit: 4ly9.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NSA BEN 0.03724 0.41443 1.26582
2 4WOE 3S5 0.002366 0.46148 2.1978
3 3SQP 3J8 0.006044 0.46583 2.30126
4 4RW3 SHV 0.04227 0.43131 2.31788
5 4L9I 8PR 0.006481 0.44119 2.38095
6 5K9B FMN 0.02751 0.40397 2.77778
7 4OAS 2SW 0.02964 0.40241 3.125
8 1I7A PHE 0.02735 0.41746 3.6036
9 2C04 GCP 0.02714 0.40715 4.86656
10 5F2T PLM 0.01382 0.41532 4.87013
11 3C0G 3AM 0.04944 0.40305 5.12821
12 5DKK FMN 0.02184 0.40596 5.51724
13 5VRH OLB 0.0235 0.43489 5.55556
14 4UP4 NDG 0.04102 0.40867 6.48379
15 4UP4 NAG 0.04102 0.40867 6.48379
16 4X1Z FUC GAL NDG 0.03639 0.40867 7.53012
17 5EK3 5PK 0.0227 0.42842 9.67742
18 3G5K BB2 0.04554 0.40181 13.6612
Feedback