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Receptor
PDB id Resolution Class Description Source Keywords
5INJ 1.4 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF PRENYLTRANSFERASE PRIB TERNARY COMPLEX TRYPTOPHAN AND DIMETHYLALLYL THIOLODIPHOSPHATE (DMSPP) STREPTOMYCES SP. RM-5-8 PRENYLTRANSFERASE TRYPTOPHAN DMSPP INDOLE-PT ABBA FAMILYFOLD STRUCTURAL GENOMICS PSI-2 PROTEIN STRUCTURE INITIATENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS NATPRO TRANSFERASE
Ref.: STRUCTURE AND SPECIFICITY OF A PERMISSIVE BACTERIAL C-PRENYLTRANSFERASE. NAT. CHEM. BIOL. V. 13 366 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TRP A:501;
Valid;
none;
submit data
204.225 C11 H12 N2 O2 c1ccc...
6C7 A:503;
Valid;
none;
submit data
262.158 C5 H12 O6 P2 S CC(=C...
TRS A:502;
Invalid;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5INJ 1.4 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF PRENYLTRANSFERASE PRIB TERNARY COMPLEX TRYPTOPHAN AND DIMETHYLALLYL THIOLODIPHOSPHATE (DMSPP) STREPTOMYCES SP. RM-5-8 PRENYLTRANSFERASE TRYPTOPHAN DMSPP INDOLE-PT ABBA FAMILYFOLD STRUCTURAL GENOMICS PSI-2 PROTEIN STRUCTURE INITIATENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS NATPRO TRANSFERASE
Ref.: STRUCTURE AND SPECIFICITY OF A PERMISSIVE BACTERIAL C-PRENYLTRANSFERASE. NAT. CHEM. BIOL. V. 13 366 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 5INJ - 6C7 C5 H12 O6 P2 S CC(=CCSP(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 5INJ - 6C7 C5 H12 O6 P2 S CC(=CCSP(=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 5INJ - 6C7 C5 H12 O6 P2 S CC(=CCSP(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TRP; Similar ligands found: 29
No: Ligand ECFP6 Tc MDL keys Tc
1 DTR 1 1
2 TRP 1 1
3 LTN 0.765957 0.777778
4 TR7 0.666667 0.833333
5 3IL 0.666667 0.75
6 4Z9 0.666667 0.75
7 FT6 0.561404 0.888889
8 IAC 0.538462 0.787879
9 TSR 0.529412 0.722222
10 IOP 0.518519 0.764706
11 R59 0.515152 0.72093
12 R38 0.515152 0.72093
13 3IB 0.491228 0.742857
14 ITW 0.491228 0.694444
15 IAD 0.484375 0.738095
16 TRP GLY 0.476923 0.704545
17 TSS 0.471698 0.666667
18 CTE 0.467742 0.888889
19 DTE 0.467742 0.888889
20 IAV 0.461538 0.738095
21 IAG 0.459016 0.738095
22 LYS TRP 0.432432 0.673913
23 78U 0.42623 0.794118
24 0ZN 0.421687 0.673913
25 4OG 0.416667 0.8
26 X95 0.411765 0.680851
27 LSW 0.411765 0.680851
28 ASP TRP ASN 0.405063 0.673913
29 GLU ASP ASN ASP TRP ASN 0.405063 0.673913
Ligand no: 2; Ligand: 6C7; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 6C7 1 1
2 GST 0.613636 0.871795
3 GGS 0.5625 0.85
4 FPS 0.5625 0.85
5 AG8 0.464286 0.693878
6 ISY 0.452381 0.820513
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5INJ; Ligand: 6C7; Similar sites found with APoc: 140
This union binding pocket(no: 1) in the query (biounit: 5inj.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2NNQ T4B None
2 4O9S 2RY 1.39535
3 1GQG DCD 1.42857
4 1SZ0 M6P 1.48148
5 4BVA T3 1.49254
6 1ERB ETR 1.63934
7 2R5V HHH 1.7284
8 4OMJ 2TX 1.79856
9 2OFV 242 1.80505
10 3SAO NKN 1.875
11 5Z46 GST 1.94175
12 5Z46 8XL 1.94175
13 6CBN OZY 1.97531
14 2YIC TPP 1.97531
15 3OZ2 OZ2 2.01511
16 5DRB 5FJ 2.06186
17 5A3T MMK 2.46914
18 4NW6 2NS 2.47678
19 5HXI 5HN 2.63852
20 5HXI FAD 2.63852
21 4HK8 XYP XYP XYP XYP XYP XYP 2.6455
22 3LVW GSH 2.71605
23 4U0I 0LI 2.85714
24 1FO3 KIF 2.96296
25 1ODM ASV 3.02115
26 2PR5 FMN 3.0303
27 1GP6 QUE 3.08989
28 1GP6 DH2 3.08989
29 1GP6 SIN 3.08989
30 3V4S ATP 3.10078
31 4GCZ FMN 3.11688
32 4MNS 2AX 3.14465
33 3ZGJ RMN 3.2345
34 4FHD 0TT 3.26087
35 4FHD EEM 3.26087
36 4BG4 ADP 3.37079
37 5DKK FMN 3.44828
38 4D06 NAR 3.53357
39 1TFZ 869 3.7037
40 5T7I LAT NAG GAL 3.87097
41 1I06 TZL 3.88889
42 1QY1 PRZ 4.02299
43 2YG2 S1P 4.06977
44 2YG2 FLC 4.06977
45 1SQI 869 4.07125
46 1REQ DCA 4.19753
47 2WKQ FMN 4.21687
48 3OJI PYV 4.2328
49 5JO1 6LM 4.32432
50 3JRS A8S 4.32692
51 2OJW ADP 4.42708
52 1VA6 ADP 4.44444
53 1VA6 P2S 4.44444
54 2Z6D FMN 4.61538
55 3T50 FMN 4.6875
56 3OV6 MK0 4.78589
57 3VQ2 LP4 LP5 MYR DAO 4.86111
58 1TT8 PHB 4.87805
59 5DJU FMN 4.91803
60 4P8K FAD 4.93827
61 4P8K 38C 4.93827
62 4WVO 3UZ 4.97238
63 5UR6 8KM 4.97238
64 4AZP A9M 5.07246
65 2YOO K2B 5.18518
66 2P7Q GG6 5.26316
67 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 5.31915
68 2AG4 LP3 5.4878
69 2AG4 OLA 5.4878
70 3GM5 CIT 5.66038
71 3I4X DST 5.67901
72 3E85 BSU 5.6962
73 4R38 RBF 5.71429
74 1IIU RTL 5.74713
75 4ORR PE3 5.78947
76 4JH6 FCN 5.7971
77 5SVV FMN 5.83942
78 2CM4 RCL 6
79 3KDJ A8S 6.01266
80 3ZXE PGZ 6.01504
81 3VMG 9CA 6.08696
82 1YKJ PHB 6.09137
83 1YKJ FAD 6.09137
84 1OGX EQU 6.10687
85 4WUJ FMN 6.12245
86 4XCB AKG 6.13027
87 6GBV FMN 6.16438
88 6BE3 NAG 6.1674
89 2AGC DAO 6.17284
90 1U6R ADP 6.31579
91 5DEY 59T 6.39731
92 4R3U 3HC 6.66667
93 4R3U 3KK 6.66667
94 5BVT PAM 6.71642
95 4K3H 1OM 6.77966
96 4HIA FMN 6.81818
97 3PQB VGP 6.91358
98 2E56 MYR 6.94444
99 5FPX GLY SER SER HIS HIS HIS HIS HIS 7.07965
100 2QM9 TDZ 7.09677
101 1EWJ BLM 7.14286
102 4RPL 3UC 7.26817
103 1VYF OLA 7.40741
104 5HA0 LTD 7.69231
105 1SWG BTN 7.8125
106 5UMY TNN 7.85714
107 4NV7 COA 8.01282
108 5U98 1KX 8.08081
109 5FKP 6UL 8.08081
110 1ZHX HC3 8.14815
111 1QIN GIP 8.19672
112 5HZ5 65X 8.20895
113 2QL9 CIT 8.24742
114 4BVM PLM 8.27068
115 4BVM VCA 8.27068
116 3FW9 SLX 8.68687
117 2YAK OSV 8.77193
118 5HZ9 5M8 8.88889
119 1EWF PC1 9.87654
120 2ZSC BTN 9.92908
121 5EFW FMN 10
122 3E2M E2M 10.2703
123 2BOS GLA GAL 10.2941
124 2BOS GLA GAL GLC 10.2941
125 4PSB GA3 10.3226
126 3D72 FAD 10.7383
127 5W1E PHB 10.8642
128 1FDQ HXA 11.4504
129 5N87 N66 11.5016
130 3IS2 FAD 12.3377
131 1N9L FMN 12.844
132 3WG3 A2G GAL NAG FUC 12.9213
133 4BJ8 BTN 13.4921
134 4C2V YJA 13.6364
135 5D48 L96 14.4737
136 2V0U FMN 16.4384
137 5H5A 6OU 17.9167
138 2Z6C FMN 20.155
139 5IXH OTP 21.118
140 5DJT FMN 26.2295
Pocket No.: 2; Query (leader) PDB : 5INJ; Ligand: TRP; Similar sites found with APoc: 28
This union binding pocket(no: 2) in the query (biounit: 5inj.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5TZJ UD1 1.63043
2 5ZW7 FAD 1.74129
3 6HTO MET 1.75
4 6HTO 5AD 1.75
5 5Z46 8XL 1.94175
6 3HDY GDU 2.01511
7 1SGJ OAA 2.11268
8 1HDC CBO 2.3622
9 5OO5 UUA 2.41935
10 3WN0 FUB 2.46914
11 4XQC 13D 2.71605
12 4XQC NAD 2.71605
13 2C4J GSO 2.75229
14 4D5B ACX 2.94985
15 4OIV XX9 3.53982
16 1QY1 PRZ 4.02299
17 4O8O AHR 4.16667
18 4L9Z OXL 4.71976
19 3I4X DST 5.67901
20 1DZK PRZ 5.73248
21 3NHT U46 5.74324
22 5IXG OTP 5.91716
23 2QDT I38 5.94796
24 3O9L LPN 9.03614
25 3E2M E2M 10.2703
26 6G9I CXX 11.9048
27 4GYW UDP 12.8395
28 4REI 3MV 17.8808
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