Receptor
PDB id Resolution Class Description Source Keywords
3KRO 1.95 Å EC: 2.5.1.1 MINT HETEROTETRAMERIC GERANYL PYROPHOSPHATE SYNTHASE IN COMP MAGNESIUM, IPP, AND DMASPP (II) MENTHA X PIPERITA PRENYLTRANSFERASE ISOPRENE BIOSYNTHESIS ISOPRENYL PYROPHOSSYNTHASE TRANSFERASE
Ref.: STRUCTURE OF A HETEROTETRAMERIC GERANYL PYROPHOSPHA SYNTHASE FROM MINT (MENTHA PIPERITA) REVEALS INTERS REGULATION PLANT CELL V. 22 454 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DST D:2002;
Valid;
none;
submit data
264.174 C5 H14 O6 P2 S CC(C)...
EDO C:2005;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
IPE A:2003;
D:2001;
Valid;
Valid;
none;
none;
submit data
246.092 C5 H12 O7 P2 CC(=C...
MG A:3003;
A:3004;
D:3001;
D:3002;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PPV A:2004;
Valid;
none;
submit data
177.975 H4 O7 P2 OP(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KRO 1.95 Å EC: 2.5.1.1 MINT HETEROTETRAMERIC GERANYL PYROPHOSPHATE SYNTHASE IN COMP MAGNESIUM, IPP, AND DMASPP (II) MENTHA X PIPERITA PRENYLTRANSFERASE ISOPRENE BIOSYNTHESIS ISOPRENYL PYROPHOSSYNTHASE TRANSFERASE
Ref.: STRUCTURE OF A HETEROTETRAMERIC GERANYL PYROPHOSPHA SYNTHASE FROM MINT (MENTHA PIPERITA) REVEALS INTERS REGULATION PLANT CELL V. 22 454 2010
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3OAB - IPE C5 H12 O7 P2 CC(=C)CCO[....
2 3KRC - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3KRF - IPE C5 H12 O7 P2 CC(=C)CCO[....
4 3KRP - GPP C10 H20 O7 P2 CC(=CCC/C(....
5 3KRO - IPE C5 H12 O7 P2 CC(=C)CCO[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 2J1P - GRG C20 H36 O7 P2 CC(=CCC/C(....
2 3OAB - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3KRC - IPE C5 H12 O7 P2 CC(=C)CCO[....
4 3KRF - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 3KRP - GPP C10 H20 O7 P2 CC(=CCC/C(....
6 3KRO - IPE C5 H12 O7 P2 CC(=C)CCO[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 2J1P - GRG C20 H36 O7 P2 CC(=CCC/C(....
2 3OAB - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3KRC - IPE C5 H12 O7 P2 CC(=C)CCO[....
4 3KRF - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 3KRP - GPP C10 H20 O7 P2 CC(=CCC/C(....
6 3KRO - IPE C5 H12 O7 P2 CC(=C)CCO[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DST; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 DST 1 1
2 ISY 0.475 0.820513
3 IPR 0.425 0.837838
Ligand no: 2; Ligand: IPE; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 IPE 1 1
2 IP8 0.617647 0.918919
3 0O3 0.589744 0.871795
4 0CJ 0.536585 0.780488
5 P23 0.527778 0.815789
6 ISY 0.487805 0.85
7 DED 0.487179 0.653061
8 IPR 0.475 0.820513
9 P25 0.463415 0.825
10 P22 0.444444 0.710526
11 0CH 0.439024 0.731707
12 43W 0.439024 0.789474
13 EIP 0.431818 0.846154
14 DMA 0.428571 0.794872
15 0JX 0.428571 0.810811
16 0K2 0.418605 0.74359
17 BHI 0.413043 0.767442
18 DP6 0.408163 0.785714
Ligand no: 3; Ligand: PPV; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PPV 1 1
2 PIS 0.642857 0.84
3 3PO 0.6 1
4 PPK 0.473684 0.7
5 POP 0.466667 0.909091
6 XPO 0.411765 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KRO; Ligand: DST; Similar sites found: 67
This union binding pocket(no: 1) in the query (biounit: 3kro.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.0129 0.4251 None
2 2VWA PTY 0.03902 0.40227 None
3 2YOO K2B 0.01055 0.40229 2.71186
4 3SQP 3J8 0.0447 0.40135 2.91971
5 5JF2 SF7 0.004104 0.42055 3.43137
6 4OKZ 3E9 0.003034 0.40016 3.64964
7 3P2H MTA 0.02549 0.41267 4.0146
8 5CX6 CDP 0.0346 0.40475 4.0146
9 5DXG EST 0.01438 0.40993 4.21456
10 5DX3 EST 0.01828 0.40484 4.21456
11 5DXE EST 0.01747 0.4022 4.21456
12 4TUZ 36J 0.01706 0.40631 4.31373
13 4TV1 36M 0.03808 0.40011 4.38247
14 3TL1 JRO 0.03522 0.40192 4.40252
15 5VRH OLB 0.02119 0.41601 4.40678
16 4UCC ZKW 0.008164 0.44333 4.72103
17 3HSS MLA 0.0188 0.40794 5.10949
18 4KWD JF2 0.001436 0.42286 5.42373
19 3CHT 4NB 0.02789 0.40971 5.47445
20 5HCN DAO 0.01002 0.4307 5.74713
21 3SDV 911 0.001363 0.45482 5.76271
22 4W4S B29 0.002491 0.41958 5.83942
23 4WH9 3M8 0.01685 0.42908 6.01093
24 1I0B PEL 0.01414 0.43942 6.20438
25 3FW9 SLX 0.006642 0.41124 6.44068
26 5CKS GAL 0.02783 0.40821 6.56934
27 5N8V KZZ 0.02522 0.40548 7.24638
28 4V3I ASP LEU THR ARG PRO 0.00783 0.44 7.393
29 5CX8 RP3 0.0163 0.41296 7.79661
30 3G58 988 0.007069 0.41348 8.13648
31 4V2O CLQ 0.02311 0.40743 8.53659
32 5G61 FNY 0.008923 0.40888 8.75912
33 2QJY UQ2 0.01398 0.42472 9.12409
34 2AEL SAZ 0.006183 0.41263 9.49153
35 1N20 3AG 0.007078 0.40059 9.49153
36 5GUE GGS 0.007515 0.40248 9.66767
37 3P5P A3C 0.003331 0.42099 9.83051
38 5V4R MGT 0.002573 0.46948 10.4938
39 5OCA 9QZ 0.003962 0.45854 10.5839
40 2O1O RIS 0.000001702 0.63493 10.8475
41 4A01 2PN 0.03011 0.40151 10.9489
42 3KYQ DPV 0.01231 0.42601 11.0553
43 4YSX E23 0.02537 0.40947 11.1702
44 1YYE 196 0.01438 0.40624 11.194
45 5D9X GSH 0.03113 0.40664 12.1739
46 4J26 EST 0.007713 0.42311 12.5
47 3R9V DXC 0.02427 0.41276 12.5874
48 5LWY OLA 0.01064 0.40213 12.605
49 1TLG GAL 0.03158 0.40137 12.8
50 1CZA ADP 0.009634 0.43499 13.1387
51 3TDC 0EU 0.03408 0.40325 13.8686
52 3G08 FEE 0.01509 0.40425 14.1414
53 4DOO DAO 0.008396 0.41008 14.1463
54 4ZGM 32M 0.0159 0.42292 22.5806
55 5MWE TCE 0.02554 0.40931 22.8571
56 2P1C GG3 0.00000001713 0.62181 28.4746
57 1YHM AHD 0.0000001913 0.67718 29.1525
58 4DXJ IPE 0.00000000004017 0.73293 31.8644
59 4DXJ 0M9 0.00000000003143 0.73156 31.8644
60 2Z7I 742 0.000002067 0.5841 33.5593
61 4JZB P2H 0.000000008673 0.71141 37.9661
62 4JZX IPE 0.00000002704 0.68749 37.9661
63 4JZB IPE 0.00000003163 0.68418 37.9661
64 4JZX 476 0.00000005285 0.6545 37.9661
65 3LDW ZOL 0.000000001258 0.60351 37.9661
66 3LDW IPE 0.0000000392 0.5892 37.9661
67 3WJO IPE 0.000000004674 0.77313 45.4237
Pocket No.: 2; Query (leader) PDB : 3KRO; Ligand: IPE; Similar sites found: 65
This union binding pocket(no: 2) in the query (biounit: 3kro.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.0129 0.4251 None
2 2VWA PTY 0.03902 0.40227 None
3 2YOO K2B 0.01055 0.40229 2.71186
4 3SQP 3J8 0.0447 0.40135 2.91971
5 5JF2 SF7 0.004104 0.42055 3.43137
6 4OKZ 3E9 0.003034 0.40016 3.64964
7 3P2H MTA 0.02549 0.41267 4.0146
8 5CX6 CDP 0.0346 0.40475 4.0146
9 2GN2 C5P 0.009787 0.43014 4.0678
10 5DXG EST 0.01438 0.40993 4.21456
11 5DX3 EST 0.01828 0.40484 4.21456
12 5DXE EST 0.01747 0.4022 4.21456
13 4TUZ 36J 0.01706 0.40631 4.31373
14 4TV1 36M 0.03808 0.40011 4.38247
15 3TL1 JRO 0.03522 0.40192 4.40252
16 5VRH OLB 0.02119 0.41601 4.40678
17 4UCC ZKW 0.008164 0.44333 4.72103
18 3HSS MLA 0.0188 0.40794 5.10949
19 1NF8 BOG 0.03673 0.40211 5.31401
20 4KWD JF2 0.001436 0.42286 5.42373
21 5HCN DAO 0.01002 0.4307 5.74713
22 3SDV 911 0.001363 0.45482 5.76271
23 4W4S B29 0.002491 0.41958 5.83942
24 1I0B PEL 0.01414 0.43942 6.20438
25 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.02273 0.42377 6.56934
26 5CKS GAL 0.02783 0.40821 6.56934
27 4F4S EFO 0.0382 0.40004 6.57895
28 5N8V KZZ 0.02522 0.40548 7.24638
29 4V3I ASP LEU THR ARG PRO 0.00783 0.44 7.393
30 5CX8 RP3 0.0163 0.41296 7.79661
31 3G58 988 0.007069 0.41348 8.13648
32 4V2O CLQ 0.02311 0.40743 8.53659
33 5G61 FNY 0.008923 0.40888 8.75912
34 2QJY UQ2 0.01398 0.42472 9.12409
35 5GUE GGS 0.007515 0.40248 9.66767
36 3P5P A3C 0.003331 0.42099 9.83051
37 5V4R MGT 0.002573 0.46948 10.4938
38 5OCA 9QZ 0.003962 0.45854 10.5839
39 2O1O RIS 0.000001702 0.63493 10.8475
40 4A01 2PN 0.03011 0.40151 10.9489
41 3KYQ DPV 0.01231 0.42601 11.0553
42 4YSX E23 0.02537 0.40947 11.1702
43 1YYE 196 0.01438 0.40624 11.194
44 5D9X GSH 0.03113 0.40664 12.1739
45 4J26 EST 0.007713 0.42311 12.5
46 3R9V DXC 0.02427 0.41276 12.5874
47 5LWY OLA 0.01064 0.40213 12.605
48 1TLG GAL 0.03158 0.40137 12.8
49 3TDC 0EU 0.03408 0.40325 13.8686
50 3G08 FEE 0.01509 0.40425 14.1414
51 3B9Z CO2 0.04614 0.40893 15.5932
52 4ZGM 32M 0.0159 0.42292 22.5806
53 5MWE TCE 0.02554 0.40931 22.8571
54 2P1C GG3 0.00000001713 0.62181 28.4746
55 1YHM AHD 0.0000001913 0.46576 29.1525
56 4DXJ IPE 0.00000000004017 0.73293 31.8644
57 4DXJ 0M9 0.00000000003143 0.73156 31.8644
58 2Z7I 742 0.000002067 0.5841 33.5593
59 4JZB P2H 0.000000008673 0.71141 37.9661
60 4JZB IPE 0.00000003163 0.68418 37.9661
61 3LDW ZOL 0.000000001258 0.60351 37.9661
62 3LDW IPE 0.0000000392 0.5892 37.9661
63 4JZX 476 0.00000005285 0.52389 37.9661
64 4JZX IPE 0.00000002704 0.5216 37.9661
65 3WJO IPE 0.000000004674 0.77313 45.4237
Pocket No.: 3; Query (leader) PDB : 3KRO; Ligand: DST; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3kro.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3KRO; Ligand: IPE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3kro.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3KRO; Ligand: PPV; Similar sites found: 21
This union binding pocket(no: 5) in the query (biounit: 3kro.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OKZ 3E9 0.01258 0.40446 3.64964
2 3Q8G PEE 0.04617 0.40508 4.74453
3 3DGY 2GP 0.01514 0.40912 5.15464
4 2GZ3 NAP 0.04547 0.40332 6.20438
5 1S7G NAD 0.02386 0.40202 6.71937
6 2WR1 NAG 0.00002863 0.45535 6.77966
7 4TXJ THM 0.02466 0.40015 7.79661
8 2Z4T LBT 0.02389 0.40037 8.81356
9 2QJY UQ2 0.003266 0.44191 9.12409
10 5OCA 9QZ 0.002864 0.44676 10.5839
11 2I0G I0G 0.03502 0.4092 11.6732
12 2P1C GG3 0.003329 0.44086 28.4746
13 4DXJ 0M9 0.0000004842 0.62489 31.8644
14 4DXJ IPE 0.0000005896 0.62489 31.8644
15 2Z7I 742 0.0001143 0.54929 33.5593
16 4JZB IPE 0.0003211 0.47069 37.9661
17 4JZX IPE 0.0003822 0.45591 37.9661
18 3LDW IPE 0.0001564 0.41425 37.9661
19 3LDW ZOL 0.00004633 0.41207 37.9661
20 4JZB P2H 0.006342 0.41088 37.9661
21 3WJO IPE 0.00000341 0.5948 45.4237
Pocket No.: 6; Query (leader) PDB : 3KRO; Ligand: IPE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3kro.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3KRO; Ligand: PPV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3kro.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3KRO; Ligand: IPE; Similar sites found: 4
This union binding pocket(no: 8) in the query (biounit: 3kro.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DGY 2GP 0.01958 0.40912 5.15464
2 2WR1 NAG 0.00003752 0.45535 6.77966
3 3KDU NKS 0.02884 0.40298 6.85921
4 2Z4T LBT 0.02948 0.40037 8.81356
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