Receptor
PDB id Resolution Class Description Source Keywords
1YHM 2.5 Å EC: 2.5.1.10 STRUCTURE OF THE COMPLEX OF TRYPANOSOMA CRUZI FARNESYL DISPH SYNTHASE WITH ALENDRONATE, ISOPENTENYL DIPHOSPHATE AND MG+2 TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE ALENDRONATE ISOPENTENYL DIPHMEVALONATE PATWAY GERANYL TRANSFERASE DIMETHYLALLYL TRANSFPPS TRANSFERASE
Ref.: STRUCTURE AND MECHANISM OF THE FARNESYL DIPHOSPHATE FROM TRYPANOSOMA CRUZI: IMPLICATIONS FOR DRUG DESIG PROTEINS V. 62 80 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AHD A:901;
B:1901;
C:2901;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 147 uM
245.064 C4 H9 N O7 P2 C(CC(...
MG A:401;
A:402;
A:403;
B:1401;
B:1402;
B:1403;
C:2401;
C:2402;
C:2403;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:370;
B:1370;
C:2370;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
IPE A:900;
B:1900;
C:2900;
Valid;
Valid;
Valid;
none;
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
1YHM 2.5 Å EC: 2.5.1.10 STRUCTURE OF THE COMPLEX OF TRYPANOSOMA CRUZI FARNESYL DISPH SYNTHASE WITH ALENDRONATE, ISOPENTENYL DIPHOSPHATE AND MG+2 TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE ALENDRONATE ISOPENTENYL DIPHMEVALONATE PATWAY GERANYL TRANSFERASE DIMETHYLALLYL TRANSFPPS TRANSFERASE
Ref.: STRUCTURE AND MECHANISM OF THE FARNESYL DIPHOSPHATE FROM TRYPANOSOMA CRUZI: IMPLICATIONS FOR DRUG DESIG PROTEINS V. 62 80 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1YHM ic50 = 147 uM AHD C4 H9 N O7 P2 C(CC(O)(P(....
70% 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 1YHM ic50 = 147 uM AHD C4 H9 N O7 P2 C(CC(O)(P(....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1YHM ic50 = 147 uM AHD C4 H9 N O7 P2 C(CC(O)(P(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: AHD; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 AHD 1 1
2 212 0.566667 0.85
3 252 MG 0.459459 0.613636
4 H23 MG 0.459459 0.613636
5 NRD 0.428571 0.809524
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 43W 0.439024 0.789474
12 0CH 0.439024 0.731707
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 Ligands (3D)
Ligand no: 1; Ligand: AHD; Similar ligands found: 26
No: Ligand Similarity coefficient
1 210 0.9752
2 ZOL 0.9365
3 0M9 0.9241
4 DMO 0.9140
5 028 0.9062
6 RIS 0.8988
7 AOR 0.8851
8 FLC 0.8806
9 CIT 0.8791
10 HCA 0.8781
11 ICT 0.8775
12 SIF 0.8687
13 1U1 0.8654
14 1AL 0.8624
15 NZ2 0.8619
16 TRA 0.8619
17 IPM 0.8608
18 V6F 0.8607
19 EMZ 0.8604
20 7A3 0.8592
21 SF9 0.8575
22 6R8 0.8571
23 NCD 0.8551
24 KBB 0.8526
25 KG1 0.8525
26 TRC 0.8508
Ligand no: 2; Ligand: IPE; Similar ligands found: 140
No: Ligand Similarity coefficient
1 IS3 0.9735
2 10D 0.9529
3 10E 0.9483
4 H6P 0.9440
5 10G 0.9433
6 DST 0.9412
7 0CN 0.9411
8 2JA 0.9339
9 0CM 0.9331
10 43Q 0.9304
11 RGP 0.9261
12 P3S 0.9259
13 2E5 0.9200
14 2E4 0.9161
15 AZM 0.9151
16 2E6 0.9145
17 PMV 0.9124
18 DLT 0.9121
19 HPO 0.9081
20 0CG 0.9079
21 BGT 0.9058
22 6FR 0.9052
23 I58 0.9029
24 AGP 0.9018
25 G6Q 0.9009
26 MGB 0.9008
27 G88 0.9005
28 3PO 0.8983
29 DG2 0.8982
30 ATX 0.8980
31 PA5 0.8962
32 M3L 0.8957
33 58X 0.8948
34 5DS 0.8936
35 ZZU 0.8923
36 DI9 0.8915
37 STX 0.8907
38 CXA 0.8892
39 HSA 0.8888
40 DX5 0.8882
41 5SP 0.8881
42 TX4 0.8878
43 5TO 0.8855
44 NLQ 0.8854
45 88L 0.8850
46 PAN 0.8834
47 NFZ 0.8833
48 CIR 0.8833
49 PPK 0.8830
50 5RP 0.8824
51 ARG 0.8824
52 4TP 0.8823
53 ALA GLU 0.8820
54 0F3 0.8819
55 3CX 0.8813
56 GGB 0.8813
57 RES 0.8811
58 ILO 0.8811
59 GGG 0.8808
60 4NP 0.8793
61 2OR 0.8792
62 EGV 0.8790
63 PNP 0.8789
64 PAU 0.8787
65 DAR 0.8787
66 3UF 0.8784
67 NBB 0.8784
68 AHL 0.8776
69 4MB 0.8774
70 R52 0.8774
71 R5P 0.8774
72 CU0 0.8771
73 NLG 0.8757
74 M3C 0.8756
75 3W3 0.8755
76 A5P 0.8753
77 PTB 0.8753
78 GVA 0.8752
79 2J3 0.8749
80 HCT 0.8743
81 5LD 0.8743
82 GRQ 0.8736
83 64Z 0.8733
84 4NS 0.8732
85 HRG 0.8732
86 D5X 0.8731
87 VFG 0.8731
88 3EB 0.8730
89 DXP 0.8730
90 HAR 0.8728
91 HCA 0.8727
92 HLP 0.8723
93 6C5 0.8713
94 MZM 0.8712
95 ASF 0.8709
96 S6P 0.8702
97 DEZ 0.8697
98 6FG 0.8697
99 5OY 0.8693
100 CPM 0.8692
101 PML 0.8691
102 WT2 0.8690
103 1OS 0.8687
104 M28 0.8684
105 B15 0.8675
106 XOG 0.8672
107 KAP 0.8669
108 FSA 0.8669
109 6C8 0.8668
110 2O8 0.8666
111 U4G 0.8663
112 1PS 0.8661
113 5PV 0.8659
114 HJ7 0.8649
115 1FD 0.8647
116 GG8 0.8647
117 LGT 0.8646
118 GAE 0.8643
119 AES 0.8640
120 E79 0.8640
121 IOP 0.8638
122 API 0.8637
123 VUR 0.8637
124 6PG 0.8634
125 3XR 0.8622
126 DER 0.8612
127 U7E 0.8609
128 FM4 0.8605
129 4JE 0.8599
130 23N 0.8596
131 BSC 0.8587
132 GLY GLY GLY 0.8579
133 ING 0.8576
134 2JJ 0.8569
135 EUE 0.8565
136 0QA 0.8564
137 K4V 0.8541
138 LRW 0.8540
139 CS2 0.8539
140 KDG 0.8525
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YHM; Ligand: IPE; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 1yhm.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3LDW IPE 46.4088
2 3LDW IPE 46.4088
3 3LDW IPE 46.4088
4 3LDW ZOL 46.4088
5 3LDW ZOL 46.4088
Pocket No.: 2; Query (leader) PDB : 1YHM; Ligand: AHD; Similar sites found with APoc: 11
This union binding pocket(no: 2) in the query (biounit: 1yhm.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 6R4V BFQ 5.53746
2 2Z7I 742 21.4706
3 3KRO IPE 29.1525
4 3KRO DST 29.1525
5 2O1O RIS 40.0552
6 2O1O RIS 40.0552
7 3LDW ZOL 46.4088
8 3LDW ZOL 46.4088
9 3LDW ZOL 46.4088
10 3LDW IPE 46.4088
11 3LDW IPE 46.4088
Pocket No.: 3; Query (leader) PDB : 1YHM; Ligand: AHD; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 1yhm.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 6R4V BFQ 5.53746
2 2Z7I 742 21.4706
3 2O1O RIS 40.0552
4 2O1O RIS 40.0552
5 3LDW ZOL 46.4088
6 3LDW ZOL 46.4088
7 3LDW ZOL 46.4088
8 3LDW IPE 46.4088
Pocket No.: 4; Query (leader) PDB : 1YHM; Ligand: IPE; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 1yhm.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3LDW IPE 46.4088
2 3LDW IPE 46.4088
3 3LDW IPE 46.4088
4 3LDW ZOL 46.4088
5 3LDW ZOL 46.4088
Pocket No.: 5; Query (leader) PDB : 1YHM; Ligand: IPE; Similar sites found with APoc: 1
This union binding pocket(no: 5) in the query (biounit: 1yhm.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3LDW IPE 46.4088
Pocket No.: 6; Query (leader) PDB : 1YHM; Ligand: IPE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1yhm.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1YHM; Ligand: AHD; Similar sites found with APoc: 4
This union binding pocket(no: 7) in the query (biounit: 1yhm.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z7I 742 21.4706
2 2O1O RIS 40.0552
3 2O1O RIS 40.0552
4 3LDW ZOL 46.4088
Pocket No.: 8; Query (leader) PDB : 1YHM; Ligand: AHD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1yhm.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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