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Receptor
PDB id Resolution Class Description Source Keywords
3K56 2.34 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ISOPENTENYL PHOSPHATE KINASE FROM M. JA IN COMPLEX WITH IPP BETA-S METHANOCALDOCOCCUS JANNASCHII SMALL MOLECULE KINASE ATP-BINDING ATP GAMMA-S TRANSFERASEMETHANOCALDOCOCCUS JANNASCHII ISOPENTENYL MONOPHOSPHATE ISOPENTENYL DIPHOSPHATE ISOPRENOID BIOSYNTHESIS MEVALONATPATHWAY ARCHAEA
Ref.: MUTATION OF ARCHAEAL ISOPENTENYL PHOSPHATE KINASE H MECHANISM AND GUIDES PHOSPHORYLATION OF ADDITIONAL ISOPRENOID MONOPHOSPHATES. ACS CHEM.BIOL. V. 5 589 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IS3 A:300;
B:300;
Valid;
Valid;
none;
none;
submit data
264.174 C5 H14 O6 P2 S CC(C)...
SO4 A:303;
A:304;
B:301;
B:302;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3K56 2.34 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF ISOPENTENYL PHOSPHATE KINASE FROM M. JA IN COMPLEX WITH IPP BETA-S METHANOCALDOCOCCUS JANNASCHII SMALL MOLECULE KINASE ATP-BINDING ATP GAMMA-S TRANSFERASEMETHANOCALDOCOCCUS JANNASCHII ISOPENTENYL MONOPHOSPHATE ISOPENTENYL DIPHOSPHATE ISOPRENOID BIOSYNTHESIS MEVALONATPATHWAY ARCHAEA
Ref.: MUTATION OF ARCHAEAL ISOPENTENYL PHOSPHATE KINASE H MECHANISM AND GUIDES PHOSPHORYLATION OF ADDITIONAL ISOPRENOID MONOPHOSPHATES. ACS CHEM.BIOL. V. 5 589 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 3K56 - IS3 C5 H14 O6 P2 S CC(C)CCO[P....
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 3K56 - IS3 C5 H14 O6 P2 S CC(C)CCO[P....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 3LKK - IP8 C5 H11 O4 P CC(=C)CCOP....
2 3LL5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 3LL9 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 3K56 - IS3 C5 H14 O6 P2 S CC(C)CCO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IS3; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 IS3 1 1
2 IPR 0.666667 0.918919
3 EIP 0.454545 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3K56; Ligand: IS3; Similar sites found with APoc: 162
This union binding pocket(no: 1) in the query (biounit: 3k56.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2F6U CIT 1.28205
2 4P6G 2FZ 1.76991
3 6F7L FAD 1.8797
4 3IQE F42 1.8797
5 3GGO NAI 1.8797
6 3RIY NAD 1.8797
7 4XFR CIT 2.25564
8 1BDB NAD 2.25564
9 3AB1 FAD 2.63158
10 1H82 GZZ 2.63158
11 4B1W ATP 2.63158
12 5UY8 AMZ 2.63158
13 2AE2 PTO 2.69231
14 2AE2 NAP 2.69231
15 1DL5 SAH 3.00752
16 3FXU TSU 3.00752
17 1YQZ FAD 3.00752
18 2PX8 SAH 3.00752
19 1JXZ BCA 3.00752
20 1BXK NAD 3.00752
21 1NZY BCA 3.00752
22 3B6R CRN 3.38346
23 3LZW NAP 3.38346
24 3LZW FAD 3.38346
25 3KJS DQ1 3.38346
26 3KJS NAP 3.38346
27 3FC4 EDO 3.38346
28 2FR1 NDP 3.38346
29 3LAD FAD 3.38346
30 6FP4 FAD 3.38346
31 3B6C SDN 3.4188
32 2RAB FAD 3.7594
33 5G3U ITW 3.7594
34 6AM8 PLT 3.7594
35 5ZBC FAD 3.7594
36 3C6K MTA 3.7594
37 3C6K SPD 3.7594
38 4I42 1HA 3.7594
39 1KOL NAD 3.76884
40 3ITJ FAD 3.84615
41 5FPE 3TR 4.13534
42 2P41 SAH 4.13534
43 4IZC 1GZ 4.13534
44 6GAS FAD 4.13534
45 3K7M FAD 4.13534
46 1H74 ADP 4.13534
47 5THQ NDP 4.13534
48 1Q9I FAD 4.20315
49 1Q9I TEO 4.20315
50 1D4O NAP 4.34783
51 4RR7 A3S 4.41176
52 2GU8 796 4.51128
53 5TWB FAD 4.51128
54 5N5S NAP 4.51128
55 3EVG SAH 4.51128
56 2F1K NAP 4.51128
57 2ART LPA AMP 4.58015
58 4JK3 NAD 4.6332
59 1L7N ALF 4.73934
60 2NU5 NAG 4.91803
61 2HYQ MAN MAN 4.91803
62 2HYR BGC GLC 4.91803
63 2NUO BGC 4.91803
64 2GUC MAN 4.91803
65 2GUD MAN 4.91803
66 4CQM NAP 4.98084
67 6F5W KG1 5.26316
68 4LOC OXM 5.26316
69 1GPM AMP 5.26316
70 3AYI HCI 5.26316
71 3AYI FAD 5.26316
72 1WG8 SAM 5.26316
73 2JG1 ANP 5.26316
74 4AUT FAD 5.26316
75 5FI3 NAP 5.26316
76 2C6Q NDP 5.26316
77 4GNI ATP 5.26316
78 3EEL 53T 5.28634
79 4F8L AES 5.51724
80 3LM9 FRU 5.6391
81 4UCI SAM 5.6391
82 3WGT QSC 5.6391
83 3WGT FAD 5.6391
84 5HSA FAS 5.6391
85 5JJR SAH 6.01504
86 4ZUL UN1 6.01504
87 3Q9T FAY 6.01504
88 1BW9 NAD 6.01504
89 3OVR 5SP 6.14035
90 4KM2 TOP 6.14525
91 4KM2 ATR 6.14525
92 2FKA BEF 6.20155
93 1AOE GW3 6.25
94 1AOE NDP 6.25
95 5WKC TP9 6.39098
96 2BD0 NAP 6.55738
97 3ELW SAM 6.66667
98 5JIB OIA 6.76692
99 2V2V V12 6.76692
100 4B7X NAP 6.76692
101 4M7V NAP 6.85714
102 5L2Z 70C 6.89655
103 2CIG 1DG 6.91824
104 4LNU GTP 7.09534
105 5EYP GTP 7.09534
106 4EIL NDP 7.14286
107 1P4V GLY 7.5188
108 3VY6 BGC BGC 7.80142
109 3ZLB ANP 7.89474
110 3HCH RSM 8.21918
111 2VL1 GLY GLY 8.27068
112 3UOY NAP 8.27068
113 3UOY FAD 8.27068
114 1GOJ ADP 8.27068
115 5LY3 ADP 8.27068
116 1V59 FAD 8.3682
117 2J4K U5P 8.40708
118 6ASY ATP 8.64662
119 3GCZ SAM 8.64662
120 4WZA ACP 9.02256
121 2HQM FAD 9.02256
122 2VVG ADP 9.02256
123 4XTX 590 9.02256
124 4UP4 NDG 9.02256
125 1U6R IOM 9.3985
126 2CJU PHX 9.73451
127 3W5N RAM 9.77444
128 3RG9 NDP 10
129 3RG9 WRA 10
130 1J3I WRA 10.1504
131 3RYC GTP 10.4895
132 3ETG GLU 10.5263
133 3ETG GTP 10.5263
134 3ETG NDP 10.5263
135 6B2M COA 10.5263
136 4JNE ATP 10.9023
137 1PFK ADP 11.2782
138 6APL C5P 11.2782
139 6HH6 A3R 11.2782
140 2ZFZ ARG 11.3924
141 1UYY BGC BGC 11.4504
142 4YSX FAD 11.7021
143 6GAR FAD 12.782
144 4I4Z 2NE 13.1579
145 2A8X FAD 13.5338
146 1DUB CAA 13.7931
147 1VL8 NAP 14.6617
148 4DP3 MMV 15.4135
149 3TKA SAM 15.4135
150 5TTJ FAD 15.4135
151 5FUI APY 16.6667
152 4OSP NAP 16.73
153 2J5V RGP 18.0451
154 2BUP ATP 18.797
155 2BUP ADP 18.797
156 2BNF UTP 19.917
157 3EVF GTA 27.4436
158 3EVF SAH 27.4436
159 1GS5 ANP 32.9457
160 1GS5 NLG 32.9457
161 3QUR ADP 43.609
162 3QUR FM4 43.609
Pocket No.: 2; Query (leader) PDB : 3K56; Ligand: IS3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3k56.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3K56; Ligand: IS3; Similar sites found with APoc: 124
This union binding pocket(no: 3) in the query (biounit: 3k56.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 6CI9 NAP 1.1583
2 3KYF 5GP 5GP 1.2987
3 4K79 GAL A2G 1.81818
4 4CQE CQE 1.8797
5 1UWK URO 1.8797
6 1UWK NAD 1.8797
7 5EJL C2E 2.01613
8 1IT7 GUN 2.25564
9 1J2Z SOG 2.25564
10 5JKG 6LF 2.25564
11 4RKX 3S9 2.29885
12 3I3X U22 2.3166
13 2QZX IVA VAL VAL STA ALA STA 2.63158
14 2W5P CL8 2.68456
15 5XWV 8H6 2.82258
16 4L3L 5FI 3.00752
17 5AHN IMP 3.00752
18 6F97 FAD 3.00752
19 4TQK NAG 3.00752
20 3EMY IVA VAL VAL STA ALA STA 3.00752
21 1L5Y BEF 3.22581
22 1R6N 434 3.31754
23 2CDU FAD 3.38346
24 3VOZ 04A 3.38346
25 1NJR XYL 3.38346
26 3E3U NVC 3.5533
27 6GNO XDI 3.7037
28 1NAA 6FA 3.7594
29 1NAA ABL 3.7594
30 2RAB NAD 3.7594
31 5L2M 6ZY 3.7594
32 1F9V ADP 3.7594
33 5KJW 53C 3.7594
34 5J75 6GQ 3.78788
35 1COY AND 4.13534
36 1COY FAD 4.13534
37 4B9E FAH 4.13534
38 3AY6 BGC 4.51128
39 3FPZ AHZ 4.51128
40 3AY6 NAI 4.51128
41 1BZL FAD 4.51128
42 5AHM IMP 4.51128
43 3QH2 3NM 4.52489
44 2GMM MAN MAN 4.7619
45 5C9P FUC 4.88722
46 4YNU FAD 4.88722
47 4YNU LGC 4.88722
48 5T2U NAP 5.24194
49 4C2C ALA ALA ALA 5.26316
50 4Z87 GDP 5.26316
51 2HIM ASN 5.26316
52 4GN8 ASO 5.26316
53 5A1S FLC 5.26316
54 4IXH IMP 5.26316
55 1N13 AG2 5.30973
56 2QQC AG2 5.35714
57 1XL8 OCB 5.6391
58 1IZE IVA VAL VAL STA ALA STA 5.6391
59 4GKV NAD 5.6391
60 3ND6 ATP 5.84795
61 2V92 ATP 6.01504
62 1JG3 ADN 6.38298
63 3PE2 E1B 6.39098
64 2EB5 OXL 6.39098
65 2C78 PUL 6.39098
66 1TLG GAL 6.4
67 3ELW GP3 6.66667
68 1PHP ADP 6.76692
69 3GFB NAD 6.76692
70 1EZ4 NAD 6.76692
71 4ER2 IVA VAL VAL STA ALA STA 6.76692
72 1O5I NAD 6.82731
73 5N2D 8J8 6.94444
74 2GAG FAD 7.07071
75 4XDA ADP 7.14286
76 2DFV NAD 7.14286
77 1I7M CG 7.46269
78 1A5Z FBP 7.5188
79 1KQF MGD 7.5188
80 3NCQ ATP 7.56302
81 2BMZ XLM 7.80142
82 5NIU 8YZ 7.8125
83 2QE0 NAP 7.89474
84 5N2F 8HW 8.06452
85 3MVH WFE 8.27068
86 5XDT MB3 8.27068
87 4Y1B NAP 8.27068
88 4X8O AP5 8.41121
89 2QK4 ATP 9.02256
90 5A7Y SAH 9.02256
91 4JZ8 CIT 9.3985
92 6FA4 D1W 9.77444
93 2P69 PLP 9.77444
94 3G08 FEE 10.101
95 3QFA FAD 10.1504
96 2JFZ DGL 10.1961
97 3O5N BR0 10.7143
98 3A5Z KAA 10.9023
99 3A5Y KAA 10.9023
100 5BVE 4VG 11.2782
101 3OV6 MK0 11.6541
102 2F5Z FAD 12.0301
103 5TVF CGQ 12.0301
104 3RNM FAD 12.0301
105 3H4S ADP 12.5926
106 1EJ0 SAM 12.7778
107 6F3M NAD 12.782
108 1AE1 NAP 12.782
109 4M52 FAD 13.5338
110 2VVL FAD 13.5338
111 5Y4R C2E 13.9098
112 4POO SAM 14
113 4C3Y ANB 14.2857
114 3IWD M2T 14.5161
115 5C2N NAG 14.5833
116 5XLY C2E 15.0376
117 5L13 6ZE 16.9173
118 3KIF GDL 16.9811
119 5FEU NAP 18.4211
120 5FFF NAP 19.0661
121 4HA6 FAD 19.9248
122 2BNE U5P 20.7469
123 4RT1 C2E 28.5714
124 3HUJ AGH 31.3131
Pocket No.: 4; Query (leader) PDB : 3K56; Ligand: IS3; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3k56.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3K56; Ligand: IS3; Similar sites found with APoc: 7
This union binding pocket(no: 5) in the query (biounit: 3k56.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2YG3 FAD 2.63158
2 1V97 MTE 3.38346
3 2Q2V NAD 4.31373
4 5TS5 FAD 4.51128
5 2Q0L FAD 5.26316
6 1VRP IOM 9.02256
7 4Y9J UCC 9.02256
Pocket No.: 6; Query (leader) PDB : 3K56; Ligand: IS3; Similar sites found with APoc: 3
This union binding pocket(no: 6) in the query (biounit: 3k56.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2RGH FAD 3.38346
2 5EIN NAP 7.14286
3 3MF2 AMP 10.1504
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