Receptor
PDB id Resolution Class Description Source Keywords
4JZX 1.8 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE IN COMPLEX WITH 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM,C A2+ LEISHMANIA MAJOR GERANYL TRANSFERASE FPPS FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE SYNTHASE TRANSFERASE-TRANSFERASE INHIBITOR COM
Ref.: STRUCTURAL AND THERMODYNAMIC BASIS OF THE INHIBITIO LEISHMANIA MAJOR FARNESYL DIPHOSPHATE SYNTHASE BY NITROGEN-CONTAINING BISPHOSPHONATES. ACTA CRYSTALLOGR.,SECT.D V. 70 802 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:403;
B:404;
A:403;
A:404;
A:405;
B:405;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
IPE A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
246.092 C5 H12 O7 P2 CC(=C...
476 B:402;
A:402;
Valid;
Valid;
none;
none;
Kd = 198.6 nM
324.227 C11 H20 N O6 P2 CCCCc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JZX 1.8 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE IN COMPLEX WITH 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM,C A2+ LEISHMANIA MAJOR GERANYL TRANSFERASE FPPS FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE SYNTHASE TRANSFERASE-TRANSFERASE INHIBITOR COM
Ref.: STRUCTURAL AND THERMODYNAMIC BASIS OF THE INHIBITIO LEISHMANIA MAJOR FARNESYL DIPHOSPHATE SYNTHASE BY NITROGEN-CONTAINING BISPHOSPHONATES. ACTA CRYSTALLOGR.,SECT.D V. 70 802 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4JZX Kd = 198.6 nM 476 C11 H20 N O6 P2 CCCCc1ccc[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4JZX Kd = 198.6 nM 476 C11 H20 N O6 P2 CCCCc1ccc[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4JZX Kd = 198.6 nM 476 C11 H20 N O6 P2 CCCCc1ccc[....
Polypharmacology
Similar Ligands
Ligand no: 1; 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: 2; Ligand: 476; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 476 1 1
2 721 0.507937 0.821429
3 PB6 0.491803 0.875
4 722 0.470588 0.79661
5 714 0.463768 0.79661
6 B71 0.463768 0.79661
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JZX; Ligand: IPE; Similar sites found: 9
This union binding pocket(no: 1) in the query (biounit: 4jzx.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2AEL SAZ 0.01154 0.40484 3.59116
2 1W62 PYC 0.01383 0.40561 4.69613
3 2Z7I 742 0.003081 0.47885 12.0588
4 1EM6 CP4 0.03073 0.43675 17.1271
5 3WJO IPE 0.000001645 0.60576 23.1454
6 2O1O RIS 0.003597 0.43732 37.0166
7 3KRO DST 0.00000002704 0.68749 37.9661
8 3KRO IPE 0.00000002704 0.5216 37.9661
9 3KRO PPV 0.0003822 0.45591 37.9661
Pocket No.: 2; Query (leader) PDB : 4JZX; Ligand: 476; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4jzx.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4JZX; Ligand: 476; Similar sites found: 47
This union binding pocket(no: 3) in the query (biounit: 4jzx.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4S EFO 0.009556 0.41797 None
2 1I0B PEL 0.007324 0.43354 1.20482
3 5B0I BOG 0.007189 0.41053 1.45773
4 1M13 HYF 0.009692 0.4174 1.58228
5 5C2H 4PX 0.01841 0.41061 1.9337
6 5C2H 4XU 0.02161 0.40197 1.9337
7 1XMY ROL 0.01368 0.40563 2.20994
8 3G58 988 0.01344 0.4018 2.20994
9 4KWD JF2 0.005229 0.42164 2.2293
10 3G08 FEE 0.04603 0.40219 2.45614
11 4MNS 2AX 0.008154 0.43623 2.51572
12 1XRO LEU 0.01213 0.41624 2.73038
13 1YOK P6L 0.01225 0.41712 2.73438
14 2HHP FLC 0.006387 0.41539 2.76243
15 3SDV 911 0.006037 0.40995 2.76243
16 2BJ4 OHT 0.007482 0.40778 2.77778
17 2E2R 2OH 0.009786 0.42072 2.86885
18 3VRV YSD 0.02057 0.41621 2.95203
19 4DDS 0J7 0.01034 0.40318 3.04183
20 5AAV GW5 0.02556 0.41591 3.1746
21 3QCP FAD 0.01307 0.40468 3.31492
22 1N8V BDD 0.02205 0.40155 3.57143
23 4B7P 9UN 0.02651 0.4091 3.91304
24 2IYG FMN 0.01075 0.40238 4.03226
25 3JRS A8S 0.006552 0.40449 4.32692
26 4OKZ 3E9 0.002602 0.43223 4.69613
27 3CTY FAD 0.0259 0.4096 4.70219
28 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.009568 0.42545 5
29 3TL1 JRO 0.02 0.40176 5.03145
30 3MBG FAD 0.01336 0.40424 5.03597
31 5U98 1KX 0.03907 0.40848 5.05051
32 1NF8 BOG 0.03091 0.40305 5.31401
33 2J8C SPO 0.02932 0.41861 5.38462
34 1M2Z BOG 0.004236 0.44761 5.44747
35 1OQC FAD 0.01273 0.40377 5.6
36 2I0G I0G 0.03464 0.40636 5.83658
37 4URN NOV 0.02342 0.40085 7.11111
38 1RX0 2MC 0.006914 0.41755 9.11602
39 5OCA 9QZ 0.006115 0.44651 11.9048
40 2Z7I 742 0.00000004288 0.71922 12.0588
41 2CB8 MYA 0.004847 0.43605 16.092
42 3WJO IPE 0.001441 0.46738 23.1454
43 2J1P GRG 0.001516 0.4003 30.3754
44 2O1O RIS 0.000000002202 0.76093 37.0166
45 3KRO DST 0.00000005285 0.6545 37.9661
46 3KRO IPE 0.00000005285 0.52389 37.9661
47 1UBY DMA 0.00000003236 0.62233 46.9613
Pocket No.: 4; Query (leader) PDB : 4JZX; 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: 4jzx.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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