-->
Receptor
PDB id Resolution Class Description Source Keywords
5GP0 1.7 Å EC: 3.6.1.55_3.6.1.67_3.6.1.22 CRYSTAL STRUCTURE OF GERANIOL-NUDX1 COMPLEX ARABIDOPSIS THALIANA GERANIOL NUDX1 ARABIDOPSIS THALIANA COMPLEX HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE SUBSTRATE RECOGNITION OF ARABIDOPSIS GPP-BOUND NUDX1 FOR NONCANONICAL MON BIOSYNTHESIS. MOL PLANT V. 11 218 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL E:201;
I:201;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
GPP F:201;
A:201;
E:202;
I:202;
Valid;
Valid;
Valid;
Valid;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
Atoms found MORE than expected: % Diff = 2;
submit data
314.209 C10 H20 O7 P2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GP0 1.7 Å EC: 3.6.1.55_3.6.1.67_3.6.1.22 CRYSTAL STRUCTURE OF GERANIOL-NUDX1 COMPLEX ARABIDOPSIS THALIANA GERANIOL NUDX1 ARABIDOPSIS THALIANA COMPLEX HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE SUBSTRATE RECOGNITION OF ARABIDOPSIS GPP-BOUND NUDX1 FOR NONCANONICAL MON BIOSYNTHESIS. MOL PLANT V. 11 218 2018
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5GP0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 6DBZ - IPR C5 H14 O7 P2 CC(C)CCO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GPP; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 OTP 0.911111 0.95
3 FPP 0.911111 0.974359
4 VTP 0.911111 0.95
5 ZTP 0.911111 0.95
6 GRG 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 10E 0.617021 0.717391
13 10D 0.617021 0.804878
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 FPF 0.533333 0.904762
19 2CF 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 9GB 0.42 0.846154
35 FHP 0.403509 0.738095
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: 167
This union binding pocket(no: 1) in the query (biounit: 5gp0.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2D6M LBT None
2 4JH6 FCN None
3 5VKI THR NGA GAL NAG None
4 1WUW TSU None
5 3E2M E2M None
6 3ZW2 NAG GAL FUC None
7 2P7Q GG6 None
8 3E85 BSU 1.34228
9 2WPU KYT 1.34228
10 3M3E GAL A2G NPO 2.01342
11 2GJ5 VD3 2.01342
12 5H9Q TD2 2.01342
13 1Y0G 8PP 2.01342
14 6D6L FY4 2.01342
15 3EEL 53T 2.01342
16 5YLT C7N 2.01342
17 1QXW M1C 2.01342
18 2IUW AKG 2.01342
19 4EHQ GBL 2.02703
20 4WVW SLT 2.08333
21 2E56 MYR 2.08333
22 4PSB GA3 2.68456
23 2Z9V PXM 2.68456
24 4D4U FUC GAL NAG 2.68456
25 1OFZ FUL 2.68456
26 4D52 GXL 2.68456
27 3PFD FDA 2.68456
28 6GNO XDI 2.96296
29 1A78 TDG 2.98507
30 1OGX EQU 3.05344
31 5AIG VPR 3.2
32 3VQ2 LP4 LP5 MYR DAO 3.3557
33 1JQI FAD 3.3557
34 3KFF XBT 3.3557
35 3KFF ZBT 3.3557
36 3WV6 GAL BGC 3.3557
37 3WV6 GAL GLC 3.3557
38 1Y7P RIP 3.3557
39 4WOE ADP 3.3557
40 5GVL PLG 3.3557
41 5GVL GI8 3.3557
42 4X5S AZM 3.3557
43 2Q7D ANP 3.3557
44 3STD MQ0 3.3557
45 4DBH OXL 3.3557
46 1I06 TZL 3.3557
47 4OCX MT1 3.3557
48 1N5S ADL 3.57143
49 1C1L GAL BGC 3.64964
50 3VV1 GAL FUC 4.02685
51 5W0N UPU 4.02685
52 1EGD FAD 4.02685
53 3FW9 SLX 4.02685
54 3FPF MTA 4.02685
55 3FPF TNA 4.02685
56 1ZHX HC3 4.02685
57 4N14 WR7 4.02685
58 3QP8 HL0 4.02685
59 6CAY ERG 4.02685
60 4EU7 CIT 4.02685
61 3NV3 GAL NAG MAN 4.34783
62 3WUD GLC GAL 4.41176
63 1IS3 LAT 4.44444
64 5UR6 8KM 4.69799
65 2ET1 GLV 4.69799
66 6MPT C30 4.69799
67 4RF7 ARG 4.69799
68 4FHD 0TT 4.69799
69 4FHD EEM 4.69799
70 5JFS 6K0 4.69799
71 6D61 4AA 4.69799
72 5ZM4 9FU 4.69799
73 3E8N ATP 5.36913
74 3E8N VRA 5.36913
75 2CM4 RCL 5.36913
76 5VX9 FUC GAL NAG GAL BGC 5.36913
77 4P7X AKG 5.36913
78 4P7X YCP 5.36913
79 3O2K DST 5.36913
80 5DQ8 FLF 5.36913
81 6CDG PRO GLY LEU TRP LYS SER 5.36913
82 2AE2 PTO 5.36913
83 2AE2 NAP 5.36913
84 2BOS GLA GAL GLC 5.88235
85 2BOS GLA GAL 5.88235
86 4Q0P 0MK 6.04027
87 4MNS 2AX 6.04027
88 5GLT BGC GAL NAG GAL 6.04027
89 4Y9J UCC 6.04027
90 4Y9J FAD 6.04027
91 1WW5 SGA BGC 6.04027
92 6FXR AKG 6.04027
93 4QM9 CYS 6.04027
94 5IXG OTP 6.04027
95 4FFG LBS 6.04027
96 5TBM 79A 6.08696
97 5FAL SKT 6.71141
98 5FAL COA 6.71141
99 2YG2 S1P 6.71141
100 2YG2 FLC 6.71141
101 4QXB OGA 6.71141
102 5D6T NGA 6.71141
103 3ZDS HMQ 6.71141
104 4GGZ BTN 6.95652
105 5TVM PUT 7.05882
106 5TVF PUT 7.05882
107 3WUC GLC GAL 7.29927
108 5WBF LAC 7.38255
109 5NLM IOS 7.38255
110 3SLS 77D 7.38255
111 4C2X NHW 7.38255
112 5A5W GUO 7.38255
113 4JJJ CBK 7.38255
114 6CD1 PLG 7.38255
115 5ML3 DL3 8.05369
116 1EWF PC1 8.05369
117 3I8T LBT 8.72483
118 5NTW 98N 8.72483
119 5IXK 6EW 8.72483
120 4COQ SAN 8.72483
121 6B9T 2HE 8.72483
122 4RYV ZEA 9.39597
123 6B9R 2HE 9.39597
124 3PUR 2HG 9.39597
125 4OIT MAN 9.73451
126 5EZU MYR 10.1124
127 1J3R 6PG 10.7383
128 4LA7 A1O 10.7383
129 5FLJ QUE 10.7383
130 1RJW ETF 11.4094
131 1QVJ RP5 11.4094
132 3KP6 SAL 11.4094
133 5XEG AKG 11.4094
134 4RW3 IPD 11.4094
135 5I8T LAC 12.0805
136 5Y9D FAD 12.0805
137 2HZQ STR 12.0805
138 2VFT SOR 12.0805
139 2FUE M1P 12.7517
140 3KJS DQ1 12.7517
141 5KEW 6SB 13.1944
142 3KDM TES 13.4228
143 4K3H 1OM 13.5593
144 2YMZ LAT 13.8462
145 1VYF OLA 14.0741
146 2ZJ1 ARJ 14.094
147 2ZJ1 NAD 14.094
148 1Q23 FUA 14.7651
149 5EYK 5U5 15.2542
150 1NWW HPN 15.4362
151 5NFB 8VT 15.4362
152 6FOF LAT 15.4362
153 2VBF TPP 16.1074
154 1QMG DMV 16.1074
155 2IID PHE 16.7785
156 2IID FAD 16.7785
157 5DEQ ARA 16.7785
158 3SCH TB6 19.4631
159 2I8T GDD 20.1342
160 3ZUY TCH 21.4765
161 3A6T 8OG 24.031
162 3GZ8 APR 24.8322
163 5LY1 PPI 28.5714
164 5ANU 58T 36.9128
165 5HZX 2GE 40.9396
166 5ISY NAD 40.9396
167 6EHH 2GE 41.6107
Pocket No.: 2; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: 80
This union binding pocket(no: 2) in the query (biounit: 5gp0.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5IXH OTP None
2 1ULE GLA GAL NAG None
3 5HA0 LTD None
4 4WN5 MVC None
5 3BRN SRO None
6 4K55 H6P None
7 4R5Z SIN 1.34228
8 1M5W DXP 1.34228
9 5KF9 ACO 1.34228
10 1QIN GIP 2.01342
11 3OYW TDG 2.23881
12 1KGI T4A 2.3622
13 2WSA 646 2.68456
14 2WSA MYA 2.68456
15 3RGA ILD 2.68456
16 3N0Y APC 2.68456
17 3W68 VIV 2.68456
18 2ICK DMA 2.68456
19 3WLV AZA 2.68456
20 1XPK HMG 2.68456
21 2HKA C3S 3.07692
22 3JDW ORN 4.02685
23 4ZUL UN1 4.02685
24 4D1J DGJ 4.02685
25 2X32 OTP 4.02685
26 1DZK PRZ 4.02685
27 2WYA HMG 4.02685
28 1V8B ADN 4.02685
29 2XIQ MLC 4.02685
30 1TB3 FMN 4.02685
31 4V24 GYR 4.69799
32 4OMJ 2TX 4.69799
33 5YBN AKG 4.69799
34 4GJ3 0XP 4.69799
35 5ZM4 AKG 4.69799
36 1YRO UDP 4.87805
37 2A4W BLM 5.07246
38 3ZRR PXG 5.36913
39 4J7Q B7N 5.36913
40 3GL0 HXX 5.36913
41 5LGA 6VH 5.36913
42 2GQS ADP 5.36913
43 1IIU RTL 5.36913
44 2BS5 BGC GAL FUC 5.55556
45 4OPC FDA 6.04027
46 4OPC PGT 6.04027
47 2WA4 069 6.04027
48 2HUI GLV 6.04027
49 3MTX PGT 6.04027
50 4BLW SAH 6.04027
51 2HJ4 PNZ 6.04027
52 3R6U CHT 6.71141
53 3SAO NKN 6.71141
54 1QPB TPP 6.71141
55 1YKD CMP 6.71141
56 1ZOA 140 6.71141
57 3H22 B53 7.38255
58 2FTB OLA 8
59 5BSR AMP 8.05369
60 5BSR COA 8.05369
61 2JLD AG1 8.05369
62 6GBV FMN 8.21918
63 1FDQ HXA 8.39695
64 4NZN 2OU 8.72483
65 4NZN ANP 8.72483
66 1ZZ7 S0H 9.39597
67 6CGD GNP 9.39597
68 4ZJS 4P0 9.39597
69 2WCJ M21 9.92908
70 5A89 FMN 10.0671
71 5A89 ADP 10.0671
72 4EWH T77 10.7383
73 2YIP YIO 12.3188
74 3B1Q NOS 13.4228
75 3STK PLM 13.6364
76 2NNQ T4B 13.7405
77 6GNF QPS 14.7651
78 1Z2P I3S 16.7785
79 1Z2P ACP 16.7785
80 4BKS X6C 25.7732
Pocket No.: 3; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: 50
This union binding pocket(no: 3) in the query (biounit: 5gp0.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4NJH 2K8 None
2 4NJH SAM None
3 5DX9 T6P 1.34228
4 5I0U DCY 2.01342
5 6FE1 V14 2.01342
6 3NUG NAD 2.01342
7 3WDX BGC BGC GLC 2.68456
8 4D52 GIV 2.68456
9 3FV1 DYH 2.68456
10 1YNH SUO 2.68456
11 5OO5 UUA 3.22581
12 5FBN 5WF 3.3557
13 4RPO T6C 3.3557
14 4I9B 1KA 3.3557
15 2ZMF CMP 3.3557
16 2OVD DAO 4.02685
17 2BJU IH4 4.02685
18 4M1U A2G MBG 4.02685
19 2XXP DSL 4.02685
20 5VC5 96M 4.02685
21 2ZSC BTN 4.25532
22 3RDO BTN 4.69799
23 2VK4 TPP 4.69799
24 5JSP DQY 5.36913
25 4Q0A 4OA 5.36913
26 4TWL ASC 5.36913
27 5EO8 TFU 5.36913
28 1OBD AMP 5.36913
29 2PNC CLU 5.36913
30 1DY4 SNP 6.04027
31 3HAZ NAD 6.04027
32 3MBI HSX 6.71141
33 5CEO 50D 6.71141
34 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 6.71141
35 4G7A AZM 7.38255
36 1W6O LAT 7.46269
37 4UWJ MYA 8.05369
38 4UWJ 7L5 8.05369
39 2XK9 XK9 8.05369
40 3FP0 FP0 8.72483
41 4ITH RCM 8.72483
42 1REQ DCA 8.72483
43 4EKV BTN 9.39597
44 2ZID GLC GLC GLC 10.0671
45 4J36 1HR 10.7383
46 1E8G FCR 10.7383
47 1ZB6 DIN 11.4094
48 1KJ1 MAN 11.9266
49 4CZ1 VNJ 15.4362
50 2R5N TPP 28.8591
Pocket No.: 4; Query (leader) PDB : 5GP0; Ligand: GPP; 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: 5gp0.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: 63
This union binding pocket(no: 5) in the query (biounit: 5gp0.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU None
2 5T7I LAT NAG GAL None
3 3EXS 5RP 1.34228
4 2AGC DAO 2.01342
5 2REG CHT 2.68456
6 5TZO 7V7 2.68456
7 5XQW 8EU 2.68456
8 1OFZ FUC 2.68456
9 5J6Y GLC 3.3557
10 5J6Y BGC 3.3557
11 2FXU ATP 3.3557
12 1QM5 PLP 3.3557
13 2VL1 GLY GLY 3.3557
14 4YLZ LAT NAG GAL 3.3557
15 5YSQ INS 3.3557
16 1BHX ASP PHE GLU GLU ILE 3.80952
17 2GVV DI9 4.02685
18 1P4C FMN 4.02685
19 3BPX SAL 4.05405
20 5DRB 5FJ 4.69799
21 4C2W ANP 4.69799
22 6F5U CQN 4.69799
23 1IA9 ANP 4.69799
24 5OES ADP 4.69799
25 4YZC STU 4.69799
26 5WZE PRO 5.36913
27 1Q11 TYE 5.36913
28 4H69 10Y 5.36913
29 3PPQ CHT 6.04027
30 2J5B TYE 6.04027
31 3WG3 A2G GAL NAG FUC 6.04027
32 1KY8 NAP 6.04027
33 4RP9 ASC 7.38255
34 6GKV F2W 7.38255
35 2IZ1 ATR 7.38255
36 1MEX RAC 7.38255
37 2RDE C2E 8.05369
38 5E62 Z3Q GAL 5N6 8.72483
39 5J75 6GQ 9.09091
40 1IGJ DGX 9.39597
41 2W5P CL8 9.39597
42 5TFZ 7BC 10.6667
43 5GG9 8GT 12.7517
44 1GQG DCD 13.4228
45 1KHZ ADV 14.094
46 5H9P TD2 14.094
47 2H7C SIA 16.1074
48 2CDO GAL AAL GAL AAL GAL AAL 16.1074
49 3I7V ATP 17.9104
50 6BGC BGC 18.1208
51 3UXL CFI 19.4631
52 1NFS DED 20.1342
53 3X0K AR6 21.4765
54 5NQR 958 22.1477
55 2O1C PPV 22.8188
56 2QJT AMP 22.8188
57 1MK1 APR 22.8188
58 1SU2 ATP 24.1611
59 1I7Q BEZ 24.1611
60 5C8L GLC 24.8322
61 2YVO AMP 25.2747
62 1VC9 ATP 26.9841
63 2FVV IHP 30.2013
Pocket No.: 6; Query (leader) PDB : 5GP0; Ligand: GPP; 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: 5gp0.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5GP0; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5gp0.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5GP0; Ligand: GPP; 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: 5gp0.bio3) has 21 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback