Receptor
PDB id Resolution Class Description Source Keywords
4JZB 1.9 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE IN COMPLEX WITH 1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-3- P HENYLPYRIDINIUM, IPP AND CA2+ LEISHMANIA MAJOR GERANYL TRANSFERASE FPPS FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE SYNTHASE CYTOSOLIC TRANSFERASE-TRANSFERASE INCOMPLEX
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
P2H B:402;
A:405;
Valid;
Valid;
none;
none;
Kd = 342.5 nM
360.216 C13 H16 N O7 P2 c1ccc...
CA B:403;
B:404;
A:402;
A:403;
A:401;
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...
NA B:406;
A:406;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
IPE A:404;
B:401;
Valid;
Valid;
none;
none;
submit data
246.092 C5 H12 O7 P2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JZB 1.9 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE IN COMPLEX WITH 1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)-3- P HENYLPYRIDINIUM, IPP AND CA2+ LEISHMANIA MAJOR GERANYL TRANSFERASE FPPS FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE SYNTHASE CYTOSOLIC TRANSFERASE-TRANSFERASE INCOMPLEX
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 4JZB Kd = 342.5 nM P2H C13 H16 N O7 P2 c1ccc(cc1)....
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 4JZB Kd = 342.5 nM P2H C13 H16 N O7 P2 c1ccc(cc1)....
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 4JZB Kd = 342.5 nM P2H C13 H16 N O7 P2 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: P2H; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 P2H 1 1
2 364 0.763636 1
3 NI9 0.518519 0.867925
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JZB; Ligand: IPE; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 4jzb.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2AEL SAZ 0.01454 0.40008 3.59116
2 2Z7I 742 0.002825 0.48086 12.0588
3 1EM6 CP4 0.02724 0.43968 17.1271
4 3WJO IPE 0.000002396 0.59603 23.1454
5 2O1O RIS 0.002449 0.44592 37.0166
6 3KRO IPE 0.00000003163 0.68418 37.9661
7 3KRO DST 0.00000003163 0.68418 37.9661
8 3KRO PPV 0.0003211 0.47069 37.9661
Pocket No.: 2; Query (leader) PDB : 4JZB; Ligand: IPE; 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: 4jzb.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4JZB; Ligand: P2H; 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: 4jzb.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4JZB; Ligand: P2H; Similar sites found: 25
This union binding pocket(no: 4) in the query (biounit: 4jzb.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CSD ACD 0.03614 0.40353 None
2 4KWD JF2 0.002415 0.44598 2.2293
3 1YOK P6L 0.01944 0.41433 2.73438
4 3VRV YSD 0.04312 0.40619 2.95203
5 5GIC DLC 0.02714 0.40029 3.2
6 4TMK T5A 0.01573 0.41566 3.28639
7 2IYG FMN 0.005662 0.41084 4.03226
8 3ANP DCC 0.01533 0.4113 4.41176
9 4OKZ 3E9 0.01091 0.41119 4.69613
10 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.002798 0.46008 5
11 3MBG FAD 0.01211 0.41358 5.03597
12 1OQC FAD 0.01962 0.40046 5.6
13 3V1V GST 0.009869 0.40613 5.80111
14 5GUE GGS 0.00301 0.43619 6.64653
15 2Q4X HMH 0.01945 0.40124 7.23982
16 4ZCW 4NG 0.01096 0.40199 8.01105
17 4OIV XX9 0.04061 0.40092 9.73451
18 5OCA 9QZ 0.01069 0.4184 11.9048
19 2Z7I 742 0.0000002244 0.6999 12.0588
20 3WJO IPE 0.001471 0.46172 23.1454
21 2O1O RIS 0.000000001972 0.7544 37.0166
22 3KRO IPE 0.000000008673 0.71141 37.9661
23 3KRO DST 0.000000008673 0.71141 37.9661
24 3KRO PPV 0.006342 0.41088 37.9661
25 1UBY DMA 0.00000002658 0.66645 46.9613
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