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Receptor
PDB id Resolution Class Description Source Keywords
3EBL 1.9 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF RICE GID1 COMPLEXED WITH GA4 ORYZA SATIVA SUBSP. JAPONICA ALPHA/BETA HYDROLASE LIPASE GIBBERELLIN SIGNALING PATHWAYHYDROLASE NUCLEUS RECEPTOR HYDROLASE RECEPTOR
Ref.: STRUCTURAL BASIS FOR GIBBERELLIN RECOGNITION BY ITS GID1. NATURE V. 456 520 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GA4 A:401;
B:401;
C:401;
D:401;
E:401;
F:401;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 0.5 uM
332.391 C19 H24 O5 C[C@@...
MPD A:501;
B:501;
C:501;
D:501;
E:501;
F:501;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
NO3 A:601;
A:602;
A:603;
A:604;
B:601;
B:602;
B:604;
C:601;
C:602;
C:603;
C:604;
D:601;
D:602;
D:603;
E:601;
F:601;
F:602;
F:603;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.005 N O3 [N+](...
PO4 B:701;
E:701;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EBL 1.9 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF RICE GID1 COMPLEXED WITH GA4 ORYZA SATIVA SUBSP. JAPONICA ALPHA/BETA HYDROLASE LIPASE GIBBERELLIN SIGNALING PATHWAYHYDROLASE NUCLEUS RECEPTOR HYDROLASE RECEPTOR
Ref.: STRUCTURAL BASIS FOR GIBBERELLIN RECOGNITION BY ITS GID1. NATURE V. 456 520 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 3EBL Kd = 0.5 uM GA4 C19 H24 O5 C[C@@]12[C....
2 3ED1 - GA3 C19 H22 O6 C[C@@]12[C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 3EBL Kd = 0.5 uM GA4 C19 H24 O5 C[C@@]12[C....
2 3ED1 - GA3 C19 H22 O6 C[C@@]12[C....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 3EBL Kd = 0.5 uM GA4 C19 H24 O5 C[C@@]12[C....
2 3ED1 - GA3 C19 H22 O6 C[C@@]12[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GA4; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GA4 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: 100
This union binding pocket(no: 1) in the query (biounit: 3ebl.bio8) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1UO4 PIH None
3 1A8S PPI 1.4652
4 5WS9 OXL 1.64384
5 5OLK DTP 1.64384
6 1PEA ACM 1.64384
7 1R6N 434 1.89573
8 1YTM OXD 1.91781
9 3U1T MLI 1.94175
10 3WIR BGC 2.19178
11 1ZED PNP 2.19178
12 1P7T PYR 2.19178
13 1M13 HYF 2.21519
14 1OIJ AKG 2.32558
15 5WQJ 7N3 2.3569
16 3CV2 OXL 2.46575
17 4O4Z N2O 2.5974
18 5AE2 FAD 2.73973
19 5AE2 FYC 2.73973
20 4DXJ 0M9 2.76243
21 1XZ3 ICF 2.87356
22 5X30 HCS 3.0137
23 4MOP 2H5 3.0137
24 6CB2 OLC 3.07167
25 5V4R MGT 3.08642
26 2Q89 6CS 3.11284
27 4MRP GSH 3.28767
28 4CIB 7UZ 3.28767
29 2O1O RIS 3.28767
30 5NTP 98E 3.36134
31 3AI3 SOE 3.42205
32 6F9G PUT 3.42679
33 1N2A GTS 3.48259
34 3R9V DXC 3.4965
35 3GXO MQA 3.52304
36 5AHS COA 3.56164
37 5LX9 OLB 3.58306
38 2I74 MAN MAN MAN MAN 3.7037
39 4ITU 1HS 3.71747
40 4ITU NAI 3.71747
41 1R37 ETX 3.7464
42 3KYQ DPV 4.0201
43 3W54 RNB 4.55927
44 3UDG TMP 4.65753
45 1KNY KAN 4.65753
46 4TQK NAG 4.6798
47 3CEV ARG 4.68227
48 3MA0 XYP 4.79233
49 3RMK BML 4.81928
50 3IX1 NFM 4.96689
51 2XRH NIO 5
52 1GEG NAD 5.07812
53 1ZBQ NAD 5.19878
54 5VZ0 2BA 5.20548
55 4P8O 883 5.34759
56 6AYU F6P 5.4755
57 5Y02 HBX 5.60748
58 5Y02 MXN 5.60748
59 1XX4 BAM 5.74713
60 2GBB CIT 5.76923
61 5C9J DAO 6.06061
62 6GMN F4E 6.18557
63 3F8C HT1 6.34921
64 6BR8 PGV 6.34921
65 1RL4 BRR 6.38298
66 5EPA AKG 6.45161
67 1A8U BEZ 6.4982
68 6G7N DAL 6.60377
69 2HZL PYR 6.84932
70 5UI2 SUC 6.94006
71 5EO8 TFU 7.3955
72 5HZ9 5M8 7.40741
73 3RV5 DXC 7.86517
74 4LY9 1YY 8.76712
75 2ZJ1 ARJ 8.76712
76 2ZJ1 NAD 8.76712
77 3HB5 NAP 9.48012
78 4OGQ 7PH 9.49721
79 5OCA 9QZ 10.3175
80 4BE9 7P9 11.2329
81 3KP6 SAL 11.2583
82 2CKM AA7 12.6027
83 6CQW HI6 13.1507
84 5NN0 92H 13.4247
85 1LLF F23 13.6986
86 5EHZ 5NZ 14.2466
87 5X80 SAL 14.375
88 1MID LAP 15.3846
89 4EHQ GBL 15.5405
90 5B4T 3HR 16.1538
91 5B4T NAD 16.1538
92 5HC0 NPO 18.6301
93 5ZCO CHD 19.5652
94 5Z84 CHD 19.5652
95 1MT1 AG2 23.8938
96 2QQD AG2 24.1071
97 4V1F BQ1 29.0698
98 2Y69 CHD 30.1587
99 5AOA PPI 35.6643
100 4OB6 S2T 38.1232
Pocket No.: 2; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 3ebl.bio8) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2Y5S 78H 1.70068
2 5FS0 5JC 1.89573
3 1CZA ADP 2.07197
4 2G3F IZC 2.13777
5 1Q19 SSC 2.19178
6 1X1T NAD 2.30769
7 5IM3 DTP 2.46575
8 3CMJ SRT 2.73973
9 3V1S 0LH 2.79503
10 3H55 GLA 3
11 5TPX 7H7 3.25203
12 5MB4 NAG 3.28767
13 6B04 C6J 4.10557
14 1MRH FMC 4.18251
15 1T0S BML 4.65116
16 5EJ2 NAD 6.16883
17 5OWC AYZ 6.55738
18 2CFC KPC 8.4
19 4CNK MEU 10.9589
20 1ULM NAG NAG NAG 12.1951
Pocket No.: 3; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3ebl.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: 15
This union binding pocket(no: 4) in the query (biounit: 3ebl.bio4) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO5 PIH None
2 4UP4 GAL NAG 1.64384
3 2CIX CEJ 2.00669
4 5WBF LAC 2.22222
5 6BA2 7KM 2.37288
6 1U25 IHS 2.96736
7 3G5N PB2 4.41176
8 4CS9 AMP 6.34921
9 3ZO7 K6H 6.38298
10 5LWY OLB 6.54206
11 5OJI ISN 8.07692
12 1IUP ALQ 9.57447
13 3S5Y DGJ 12.8767
14 1X8D RNS 16.3462
15 1YRO UDP 34.9594
Pocket No.: 5; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3ebl.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3EBL; Ligand: GA4; 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: 3ebl.bio9) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: 5
This union binding pocket(no: 7) in the query (biounit: 3ebl.bio9) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4P8K 38C 2.70833
2 4P8K FAD 2.70833
3 4IP7 FLC 3.28767
4 3SFI 3SF 3.81356
5 1H8P PC 4.58716
Pocket No.: 8; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: 10
This union binding pocket(no: 8) in the query (biounit: 3ebl.bio7) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5ET3 60C None
2 3A51 VDY 2.46575
3 2CH5 NAG 4.03458
4 2CH5 NDG 4.03458
5 3HKW IX6 4.38356
6 4Q86 AMP 5.20548
7 2IDO TMP 7.22892
8 6G5J EM8 9.09091
9 1HBK COA 10.1124
10 1N13 AG2 23.8938
Pocket No.: 9; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: 5
This union binding pocket(no: 9) in the query (biounit: 3ebl.bio7) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5JOX EDG 1.91781
2 4F06 PHB 2.19178
3 5ZI9 FLC 2.30769
4 5U83 ZN8 3.30189
5 3N29 GOL 4.65753
Pocket No.: 10; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 3ebl.bio5) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 3ebl.bio6) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 3ebl.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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