Receptor
PDB id Resolution Class Description Source Keywords
1W55 2.3 Å EC: 2.7.7.60 STRUCTURE OF THE BIFUNCTIONAL ISPDF FROM CAMPYLOBACTER JEJUNI CAMPYLOBACTER JEJUNI BIFUNCTIONAL ENZYME BIOSYNTHETIC PATHWAY ISOPRENOIDS BIFUNCTIONAL NONMEVALONATE TRANSFERASE
Ref.: HEXAMERIC ASSEMBLY OF THE BIFUNCTIONAL METHYLERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE AND PROTEIN-PROTEIN ASSOCIATIONS IN THE DEOXY-XYLULOSE-DEPENDENT PATHWAY OF ISOPRENOID PRECURSOR BIOSYNTHESIS J.BIOL.CHEM. V. 279 52753 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C A:1372;
A:1373;
Valid;
Valid;
none;
none;
submit data
323.197 C9 H14 N3 O8 P C1=CN...
EDO A:1375;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GPP A:1374;
Valid;
none;
submit data
314.209 C10 H20 O7 P2 CC(=C...
MG A:1371;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1W55 2.3 Å EC: 2.7.7.60 STRUCTURE OF THE BIFUNCTIONAL ISPDF FROM CAMPYLOBACTER JEJUNI CAMPYLOBACTER JEJUNI BIFUNCTIONAL ENZYME BIOSYNTHETIC PATHWAY ISOPRENOIDS BIFUNCTIONAL NONMEVALONATE TRANSFERASE
Ref.: HEXAMERIC ASSEMBLY OF THE BIFUNCTIONAL METHYLERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE AND PROTEIN-PROTEIN ASSOCIATIONS IN THE DEOXY-XYLULOSE-DEPENDENT PATHWAY OF ISOPRENOID PRECURSOR BIOSYNTHESIS J.BIOL.CHEM. V. 279 52753 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1W55 - GPP C10 H20 O7 P2 CC(=CCC/C(....
70% 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 1W55 - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1W55 - GPP C10 H20 O7 P2 CC(=CCC/C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 C 1 1
2 CAR 1 1
3 C5P 1 1
4 CDP 0.787879 0.985507
5 CTP 0.753623 0.985507
6 CDP MG 0.724638 0.916667
7 7XL 0.689189 0.930556
8 16B 0.676471 0.930556
9 AR3 0.672131 0.842857
10 CTN 0.672131 0.842857
11 C2G 0.662338 0.943662
12 I5A 0.634921 0.828571
13 C5G 0.634146 0.930556
14 C C 0.632911 0.942857
15 CDC 0.62963 0.8375
16 CDM 0.621951 0.881579
17 CXY 0.607143 0.930556
18 TKW 0.591549 0.985507
19 C3P 0.585714 0.956522
20 5HM 0.575342 0.944444
21 U5P 0.571429 0.941176
22 CSV 0.555556 0.917808
23 CSQ 0.555556 0.917808
24 1AA 0.554348 0.893333
25 C2P 0.541667 0.942857
26 PMT 0.540816 0.860759
27 DCM 0.540541 0.902778
28 DC 0.540541 0.902778
29 DKZ 0.521127 0.733333
30 91P 0.495146 0.839506
31 FN5 0.495146 0.858974
32 DOC 0.493333 0.902778
33 ICR 0.486842 0.861111
34 5BU 0.486842 0.876712
35 2AA 0.485714 0.683673
36 MCN 0.485714 0.807229
37 GPC 0.481481 0.829268
38 G C 0.481132 0.848101
39 5FU 0.48 0.876712
40 CSF 0.476636 0.858974
41 PCD 0.464286 0.770115
42 U A C C 0.463636 0.857143
43 C5P SIA 0.458716 0.88
44 YYY 0.451219 0.890411
45 CNU 0.45 0.915493
46 UDP 0.45 0.927536
47 44P 0.448718 0.888889
48 DCP 0.447059 0.890411
49 G G G C 0.442478 0.860759
50 A G C C 0.438596 0.858974
51 V12 0.43617 0.7375
52 NUP 0.435897 0.929577
53 GCQ 0.435294 0.890411
54 UTP 0.433735 0.927536
55 A U C C 0.429752 0.846154
56 2KH 0.428571 0.901408
57 UP6 0.428571 0.887324
58 NVG 0.427083 0.719512
59 G C C C 0.423729 0.871795
60 S5P 0.423077 0.853333
61 GEO 0.418919 0.77027
62 CH 0.417722 0.956522
63 H2U 0.415584 0.861111
64 UDP UDP 0.414634 0.898551
65 FNU 0.4125 0.88
66 JW5 0.4125 0.901408
67 8GM 0.411765 0.906667
68 DCZ 0.410959 0.77027
69 LDC 0.410959 0.77027
70 UPU 0.409091 0.9
71 BMP 0.405063 0.901408
72 BMQ 0.402597 0.885714
73 UNP 0.402299 0.901408
74 8OP 0.402299 0.853333
75 U6M 0.4 0.914286
Ligand no: 2; Ligand: GPP; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 OTP 0.911111 0.95
3 ZTP 0.911111 0.95
4 VTP 0.911111 0.95
5 GRG 0.911111 0.974359
6 FPP 0.911111 0.974359
7 FFF 0.672727 0.904762
8 DSL 0.659574 0.875
9 0K3 0.659574 0.875
10 FJP 0.659574 0.897436
11 FDF 0.654545 0.880952
12 10D 0.617021 0.804878
13 10E 0.617021 0.717391
14 DMA 0.613636 0.868421
15 H6P 0.595745 0.804878
16 10G 0.583333 0.785714
17 A4S 0.545455 0.711538
18 2CF 0.533333 0.904762
19 FPF 0.533333 0.904762
20 FGG 0.52459 0.904762
21 GST 0.518519 0.878049
22 3E9 0.516129 0.926829
23 MGM 0.5 0.745098
24 FPS 0.482759 0.857143
25 GGS 0.482759 0.857143
26 FPQ 0.47619 0.804348
27 LA6 0.473684 0.926829
28 0FV 0.473684 0.926829
29 749 0.461538 0.871795
30 1NH 0.444444 0.787234
31 FII 0.444444 0.649123
32 SZH 0.432432 0.637931
33 PS7 0.426667 0.883721
34 FHP 0.403509 0.738095
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1W55; Ligand: C; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1w55.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1W55; Ligand: C; Similar sites found: 152
This union binding pocket(no: 2) in the query (biounit: 1w55.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PNO U5P 0.000001309 0.57681 None
2 3QDW NDG 0.007803 0.4554 None
3 3KPE TM3 0.02607 0.42342 None
4 3VCA PRO 0.009003 0.4382 1.07817
5 2JFV FLC 0.0328 0.41846 1.37457
6 2TOH HBI 0.0000594 0.46777 1.45773
7 1XP8 AGS 0.000008647 0.4267 1.63934
8 4Q3F TLA 0.02076 0.42833 1.7094
9 1GVF PGH 0.04219 0.40445 1.74825
10 2V9M CIT 0.00006108 0.52101 1.82482
11 1LTH FBP 0.001376 0.48639 1.88088
12 4RJK PYR 0.01488 0.47014 1.88679
13 1YBH P22 0.001158 0.40593 1.88679
14 5T63 ALA ALA ALA ALA 0.0004278 0.44604 1.90736
15 3TKA CTN 0.01864 0.46455 2.01729
16 2HCR AMP 0.01873 0.4107 2.14724
17 2NZ2 ASP 0.003166 0.45669 2.15633
18 2NZ2 CIR 0.001745 0.41156 2.15633
19 2WIC GNP 0.003855 0.40736 2.24719
20 3UBW 6SP 0.001159 0.53339 2.29885
21 4FUA PGH 0.002366 0.40723 2.32558
22 2C5S AMP 0.02842 0.40844 2.42588
23 1A5Z OXM 0.0005623 0.52222 2.50784
24 1A5Z FBP 0.001221 0.43721 2.50784
25 2JE7 XMM 0.0005684 0.42749 2.51046
26 1O9U ADZ 0.0228 0.44377 2.57143
27 2P69 PLP 0.02125 0.42293 2.61438
28 1UQX MMA 0.0007542 0.4301 2.65487
29 3I0O ADP 0.02066 0.41074 2.65487
30 3PMA SCR 0.03733 0.40695 2.7027
31 1C3M MAN MAN 0.0009439 0.45895 2.72109
32 2VMD MBG 0.002024 0.50148 2.72374
33 4C25 13P 0.001501 0.40793 2.83019
34 1JN2 SFP 0.03541 0.46918 2.95359
35 2O66 FLC 0.008347 0.44235 2.96296
36 2W8Q SIN 0.002464 0.42581 2.96496
37 1P9B HDA 0.04 0.40967 2.96496
38 5T0A A3P 0.02833 0.4029 2.96496
39 1MVQ MMA 0.0007973 0.41081 2.9661
40 5ALC TIQ 0.04632 0.40061 2.99145
41 1G6O ADP 0.00447 0.40089 3.0303
42 5D6C 57S 0.003782 0.49096 3.125
43 2GN2 C5P 0.00009447 0.48892 3.21637
44 1H16 PYR 0.03218 0.42939 3.2345
45 4CIB 7UZ 0.02539 0.41922 3.2345
46 2Z5Y HRM 0.0007681 0.41706 3.2345
47 2IMP LAC 0.006173 0.41088 3.2345
48 1NXJ GLV 0.0004531 0.48918 3.27869
49 1NXJ TLA 0.001341 0.44589 3.27869
50 1GXU 2HP 0.0000004188 0.55339 3.2967
51 2W24 LYS 0.0008169 0.41622 3.33333
52 1GU3 BGC BGC BGC BGC BGC 0.04406 0.40355 3.3557
53 1FNZ A2G 0.007424 0.40177 3.37553
54 1Z34 2FD 0.00001671 0.40413 3.40426
55 3PHQ KDO 0.0001179 0.61143 3.6036
56 3MD0 GDP 0.02377 0.41196 3.66197
57 3O03 GCO 0.001494 0.45072 3.78007
58 1XX4 BAM 0.0002437 0.51165 3.83142
59 4DN8 BMA 0.004991 0.45889 3.84615
60 3LTW HLZ 0.02258 0.42653 3.92857
61 1A8S PPI 0.02019 0.40929 4.0293
62 3GD8 BOG 0.0001061 0.56032 4.03587
63 3GD8 GOL 0.002703 0.41116 4.03587
64 1E4I NFG 0.00006707 0.45784 4.04313
65 1KC7 PPR 0.007566 0.45608 4.04313
66 4LTN FMN 0.00006057 0.4093 4.06091
67 4F8L GAL 0.0187 0.4642 4.13793
68 1UUY PPI 0.007257 0.47112 4.19162
69 3IHB TRS 0.0008101 0.55599 4.31267
70 4LO6 SIA GAL 0.0005981 0.51636 4.31267
71 1LDM OXM 0.003103 0.44674 4.55927
72 4N9Z V3L 0.01511 0.42067 4.58221
73 4AF0 MOA 0.003129 0.40899 4.58221
74 1NPL MAN 0.0002516 0.45426 4.58716
75 3ZF8 GDP 0.03364 0.40141 4.59016
76 2Q3M MLA 0.02965 0.43745 4.60123
77 5DRN 5CT 0.01774 0.45338 4.62963
78 1IZC PYR 0.0005311 0.44269 4.71976
79 9LDB OXM 0.04993 0.43119 4.81928
80 3B9Z CO2 0.00006396 0.55182 4.85175
81 5DS8 GLY 5CT GLY ALA 0.02369 0.43649 4.95496
82 5DUB GLY 5GG GLY ALA 0.03151 0.43285 4.95496
83 3VPD BUA 0.01217 0.47694 4.98221
84 3K3G MMU 0.01836 0.42362 5
85 2Q1A 2KT 0.001172 0.43042 5.11945
86 2XDQ MGX 0.04106 0.42958 5.12129
87 2BO4 FLC 0.03018 0.42533 5.12129
88 1ONX ASP 0.003361 0.40224 5.12129
89 3W54 RNB 0.002678 0.44026 5.16717
90 1G8S MET 0.03241 0.41872 5.21739
91 2X2T GAL NGA 0.0377 0.43166 5.22876
92 3VOZ 04A 0.001114 0.4469 5.39683
93 1HQL GLA MBG 0.04883 0.41451 5.44747
94 4M6T SAM 0.00005054 0.42471 5.46448
95 3KJQ B94 0.01936 0.40822 5.4878
96 3NOJ PYR 0.004552 0.45211 5.88235
97 2ZWS PLM 0.004315 0.50227 5.92992
98 1VBH PEP 0.01255 0.4339 5.92992
99 3S9K CIT 0.0003125 0.58615 5.9322
100 2CCV A2G 0.000005221 0.49885 5.94059
101 4AP9 1PS 0.001195 0.43756 5.97015
102 4MOB ADP 0.005282 0.42223 6.0241
103 3EJ0 11X 0.004197 0.45376 6.12245
104 1V8K ANP 0.0002418 0.42641 6.19946
105 1YOE RIB 0.0001599 0.43843 6.469
106 5DTF 5CT 0.04782 0.42295 6.469
107 1FBL HTA 0.002609 0.45002 6.48649
108 4M7F BM3 0.000296 0.50416 6.63717
109 2X0K PPV 0.006414 0.44512 6.80473
110 3EYK EYK 0.02557 0.42384 6.81115
111 3ZPG 5GP 0.0314 0.43607 7.00809
112 3L6R MLI 0.0362 0.42125 7.22543
113 1JGS SAL 0.004887 0.49905 7.24638
114 4BPM GSH 0.0004654 0.43373 7.30337
115 1BGV GLU 0.0001336 0.41361 7.54717
116 1ZUW DGL 0.027 0.40945 7.72059
117 2XZ3 MAL 0.001052 0.41278 7.81671
118 4WVH ASP HIS ASP ALA HIS ALA 0.04333 0.40009 7.81671
119 1SS4 GSH 0.01225 0.48235 7.84314
120 2OWZ CIT 0.01426 0.43641 8.13253
121 3EM1 TYD 0.0005493 0.43659 8.21918
122 2OFE NAG 0.01266 0.43896 8.4507
123 1DXY COI 0.00003274 0.47223 9.00901
124 1ML4 PAL 0.001679 0.43018 9.09091
125 1OD6 PNS 0.00002607 0.40023 9.375
126 1Y0L HAN 0.01633 0.45925 9.72222
127 43CA NPO 0.01917 0.46735 9.73451
128 1NME 159 0.00006103 0.508 9.78261
129 3OAZ 2M5 0.01038 0.47486 9.85915
130 1RYD GLC 0.01274 0.43884 10.2426
131 1NU4 MLA 0.003313 0.50912 10.3093
132 1ZX5 LFR 0.01772 0.40072 10.3333
133 3F8C HT1 0.0225 0.42173 11.1111
134 1J2Z SOG 0.003179 0.43099 11.4815
135 3CH5 GDP 0.0006965 0.40712 11.5385
136 1V5F FAD 0.001801 0.40815 11.5903
137 1V5F TPP 0.001801 0.40815 11.5903
138 2HVK TBA 0.00002854 0.56901 11.7925
139 4M7J KDA KDO KDO 0.01907 0.43847 11.8721
140 2BZ1 TAU 0.02156 0.46048 12.2449
141 3F81 STT 0.02397 0.44257 12.5683
142 4TMK T5A 0.001019 0.40489 12.6761
143 4ODV GP1 Z9M 0.0005912 0.55369 13.0233
144 4LBP 1WG 0.0009668 0.41392 15
145 3I8T LBT 0.002125 0.46468 15.8537
146 2ZO9 MLI 0.01539 0.41439 16.0584
147 1VCO GLN 0.0003613 0.43393 17.2507
148 1PTR PRB 0.01259 0.4448 20
149 1Y7P RIP 0.02429 0.42495 21.5247
150 1H8G CHT 0.03375 0.44873 25.2632
151 1JOT GAL A2G 0.002387 0.45171 26.3158
152 2UZH CDP 0.0007478 0.41751 49.0909
153 1IV2 CDP 0.000005538 0.52332 50
Pocket No.: 3; Query (leader) PDB : 1W55; Ligand: GPP; Similar sites found: 104
This union binding pocket(no: 3) in the query (biounit: 1w55.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PNO U5P 0.000001798 0.51153 None
2 3KPE TM3 0.0004132 0.46577 None
3 3QDW A2G 0.005099 0.43942 None
4 3QDT A2G GAL 0.009351 0.41928 None
5 3QDY A2G GAL 0.00996 0.41799 None
6 3QDV A2G 0.02314 0.40704 None
7 4MFL MFK 0.01266 0.4593 0.869565
8 2BLE 5GP 0.004282 0.43966 1.3624
9 1LTH FBP 0.0001706 0.48246 1.88088
10 1LTH OXM 0.001494 0.41745 1.88088
11 5T63 ALA ALA ALA ALA 0.00001053 0.43314 1.90736
12 1ZFJ IMP 0.00008991 0.53197 2.15633
13 2GRU NAD 0.02614 0.40572 2.17391
14 2FWP CIT 0.0005862 0.44871 2.18579
15 3G9E RO7 0.005993 0.49644 2.21402
16 3W8X FAD 0.0009576 0.53333 2.42588
17 3FPZ AHZ 0.0001816 0.50978 2.45399
18 1A5Z OXM 0.008628 0.42093 2.50784
19 1A5Z FBP 0.0001118 0.41187 2.50784
20 2R68 SUP 0.002191 0.49059 2.69542
21 1C3M MAN MAN 0.001347 0.4092 2.72109
22 2VMD MBG 0.001915 0.46029 2.72374
23 1JN2 SFP 0.00002211 0.47274 2.95359
24 1B7H LYS NLE LYS 0.01624 0.43916 2.96496
25 2PAR TMP 0.00001071 0.53362 2.98507
26 5D6C 57S 0.00905 0.43108 3.125
27 1BZL FAD 0.03104 0.40079 3.2345
28 1NXJ GLV 0.002831 0.41198 3.27869
29 1GXU 2HP 0.0000006987 0.4627 3.2967
30 3SUC ATP 0.000006902 0.53512 3.50404
31 2GOU FMN 0.04418 0.40517 3.56164
32 3PHQ KDO 0.0001525 0.55441 3.6036
33 1U3G THF 0.001144 0.48729 3.7037
34 1OMZ UD2 0.001719 0.44441 3.75427
35 3O03 GCO 0.01565 0.41544 3.78007
36 4DN8 BMA 0.009637 0.40627 3.84615
37 4N02 FNR 0.007355 0.42532 3.92157
38 2DQU CPD 0.004266 0.41289 4.01786
39 3GD8 BOG 0.00116 0.46194 4.03587
40 3GD8 GOL 0.00003327 0.40614 4.03587
41 1E4I NFG 0.0000001193 0.45623 4.04313
42 1UUY PPI 0.0005354 0.48742 4.19162
43 1R0X ATP 0.0007332 0.4477 4.1958
44 4LO6 SIA GAL 0.0003779 0.48017 4.31267
45 4HGP KDO 0.0005946 0.45392 4.44444
46 2FAV APR 0.01768 0.44255 4.44444
47 2QIA U20 0.01914 0.40826 4.58015
48 1NPL MAN 0.0000001509 0.48106 4.58716
49 2Q3M MLA 0.01446 0.41714 4.60123
50 5DRN 5CT 0.0004623 0.4959 4.62963
51 5DSC GLY 5CT GLY SER GLY 0.01437 0.40144 4.65116
52 1IZC PYR 0.0000002204 0.48416 4.71976
53 4EIP FAD 0.03453 0.4347 4.85175
54 5DUB GLY 5GG GLY ALA 0.001882 0.45625 4.95496
55 5DS8 GLY 5CT GLY ALA 0.01367 0.41149 4.95496
56 3VPD BUA 0.001449 0.49643 4.98221
57 2FMD MAN MAN 0.003155 0.40448 5
58 3VOZ 04A 0.0001314 0.42789 5.39683
59 5T85 44G 0.005802 0.42553 5.52147
60 1HFA PIO 0.02321 0.44902 5.53633
61 2ZPA ACO 0.008216 0.45426 5.66038
62 2YD6 FLC 0.008764 0.44216 5.66038
63 1DMR PGD 0.01589 0.43145 5.66038
64 3NOJ PYR 0.00000407 0.41413 5.88235
65 2C42 PYR 0.02646 0.44833 5.92992
66 4NTX AMR 0.005066 0.40981 5.92992
67 2CCV A2G 0.00000004267 0.46994 5.94059
68 3EJ0 11X 0.00000193 0.42314 6.12245
69 2Q2Y ADP 0.008957 0.46392 6.26703
70 1FM9 570 0.002187 0.5105 6.30252
71 4G1V FAD 0.00001292 0.56902 6.469
72 5DTF 5CT 0.001216 0.46534 6.469
73 4M7F BM3 0.0005644 0.44573 6.63717
74 1RRC ADP 0.0001466 0.45781 6.64452
75 1ULE GLA GAL NAG 0.007901 0.42273 6.66667
76 3NYQ AMP 0.0331 0.42596 6.73267
77 3NYQ MCA 0.03196 0.42596 6.73267
78 1JGS SAL 0.0266 0.41895 7.24638
79 2BGM NAJ 0.01022 0.42224 7.55396
80 1SS4 GSH 0.005476 0.45688 7.84314
81 2CW6 3HG 0.0235 0.40671 9.39597
82 1Y0L HAN 0.01573 0.42284 9.72222
83 43CA NPO 0.0189 0.43021 9.73451
84 1NME 159 0.002221 0.40146 9.78261
85 3OAZ 2M5 0.0003159 0.51629 9.85915
86 4JCA CIT 0.03767 0.40315 10.1796
87 1NU4 MLA 0.003413 0.4088 10.3093
88 3SQG COM 0.01068 0.43152 10.7817
89 2V5E SCR 0.009149 0.43499 10.8911
90 4OYA 1VE 0.01154 0.43844 11.3208
91 1V5F FAD 0.005663 0.46538 11.5903
92 1V5F TPP 0.005663 0.46538 11.5903
93 2HVK TBA 0.0001433 0.48575 11.7925
94 1JAC AMG 0.005798 0.44518 12.0301
95 2BZ1 TAU 0.02928 0.41667 12.2449
96 3F81 STT 0.02944 0.40184 12.5683
97 4TMK T5A 0.00002531 0.56298 12.6761
98 1JA9 NDP 0.001323 0.467 12.7737
99 4ODV GP1 Z9M 0.001146 0.49281 13.0233
100 3ZJ0 ACO 0.004494 0.44466 14.0777
101 2BMK PDD 0.007741 0.4134 15.493
102 3I8T LBT 0.0005398 0.44651 15.8537
103 1JOT GAL A2G 0.000004276 0.51378 26.3158
104 2UZH IPE 0.00001159 0.40716 49.0909
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