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 218 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 176 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 143 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: 35
This union binding pocket(no: 1) in the query (biounit: 3ebl.bio8) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO4 PIH 0.02091 0.41167 None
2 1A8S PPI 0.02806 0.40584 1.4652
3 1PEA ACM 0.02571 0.40818 1.64384
4 1YTM OXD 0.02188 0.40185 1.91781
5 3WIR BGC 0.02031 0.41043 2.19178
6 1P7T PYR 0.01837 0.4017 2.19178
7 1M13 HYF 0.002686 0.42878 2.21519
8 3CV2 OXL 0.02311 0.40134 2.46575
9 4O4Z N2O 0.02159 0.41651 2.5974
10 5V4R MGT 0.01026 0.42055 3.08642
11 2Q89 6CS 0.01383 0.41273 3.11284
12 4MRP GSH 0.01111 0.43274 3.28767
13 4CIB 7UZ 0.02562 0.40349 3.28767
14 2O1O RIS 0.02926 0.40065 3.28767
15 5AHS COA 0.009674 0.41202 3.56164
16 2I74 MAN MAN MAN MAN 0.02775 0.40158 3.7037
17 4S00 AKR 0.02367 0.40527 3.83562
18 3KYQ DPV 0.01664 0.41306 4.0201
19 3W54 RNB 0.01409 0.40051 4.55927
20 3UDG TMP 0.008089 0.43585 4.65753
21 3MA0 XYP 0.02332 0.40546 4.79233
22 3IX1 NFM 0.0283 0.4011 4.96689
23 2XRH NIO 0.01696 0.4061 5
24 1XX4 BAM 0.04421 0.40627 5.74713
25 1RL4 BRR 0.01824 0.40667 6.38298
26 1A8U BEZ 0.03364 0.40061 6.4982
27 1VPD TLA 0.004039 0.44956 8.69565
28 5OCA 9QZ 0.004787 0.4326 10.3175
29 4BE9 7P9 0.02732 0.40198 11.2329
30 3KP6 SAL 0.005173 0.44254 11.2583
31 4M0F 1YK 0.0001901 0.47892 13.1507
32 5DYW 5HF 0.0007391 0.45177 13.4247
33 1MT1 AG2 0.03061 0.40286 23.8938
34 5AOA PPI 0.0005945 0.47647 35.6643
35 4OB6 S2T 0.0002509 0.47653 38.1232
Pocket No.: 2; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3ebl.bio8) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 3ebl.bio4) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.02409 0.40328 None
2 2Y5S 78H 0.01472 0.40331 1.70068
3 3CMJ SRT 0.02024 0.40391 2.73973
4 1MRH FMC 0.02117 0.40764 4.18251
5 1X8D RNS 0.02946 0.40176 16.3462
6 1YRO UDP 0.03854 0.40012 34.9594
Pocket No.: 5; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 3
This union binding pocket(no: 5) in the query (biounit: 3ebl.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2G3F IZC 0.02646 0.4052 2.13777
2 3V1S 0LH 0.001562 0.47614 2.79503
3 2CFC KPC 0.03179 0.40013 8.4
Pocket No.: 6; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3ebl.bio9) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 6
This union binding pocket(no: 8) in the query (biounit: 3ebl.bio7) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3A51 VDY 0.01417 0.40409 2.46575
2 4IP7 FLC 0.02146 0.40733 3.28767
3 3GXO MQA 0.02232 0.40225 3.52304
4 2CH5 NAG 0.00544 0.42395 4.03458
5 2CH5 NDG 0.005758 0.42277 4.03458
6 2IDO TMP 0.02974 0.40094 7.22892
Pocket No.: 9; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 3ebl.bio7) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 1
This union binding pocket(no: 11) in the query (biounit: 3ebl.bio6) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JOX EDG 0.02022 0.40441 1.91781
Pocket No.: 12; Query (leader) PDB : 3EBL; Ligand: GA4; Similar sites found: 1
This union binding pocket(no: 12) in the query (biounit: 3ebl.bio3) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G5N PB2 0.02664 0.40588 4.41176
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