Receptor
PDB id Resolution Class Description Source Keywords
1WDD 1.35 Å EC: 4.1.1.39 CRYSTAL STRUCTURE OF ACTIVATED RICE RUBISCO COMPLEXED WITH 2 CARBOXYARABINITOL-1,5-BISPHOSPHATE ORYZA SATIVA JAPONICA GROUP RUBISCO PHOTOSYNTHESIS ALPHA/BETA BARREL N-METHYLMETHIONITRANSLATIONAL MODIFICATION LYASE
Ref.: CRYSTAL STRUCTURE OF RICE RUBISCO AND IMPLICATIONS ACTIVATION INDUCED BY POSITIVE EFFECTORS NADPH AND 6-PHOSPHOGLUCONATE J.MOL.BIOL. V. 422 75 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CAP A:1001;
E:2001;
Valid;
Valid;
none;
none;
submit data
356.115 C6 H14 O13 P2 C([C@...
GOL A:3001;
A:3004;
A:3006;
A:3010;
A:3012;
A:3015;
A:3017;
E:3002;
E:3003;
E:3005;
E:3009;
E:3011;
E:3013;
E:3014;
E:3016;
W:3007;
W:3008;
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;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:1476;
E:2476;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1WDD 1.35 Å EC: 4.1.1.39 CRYSTAL STRUCTURE OF ACTIVATED RICE RUBISCO COMPLEXED WITH 2 CARBOXYARABINITOL-1,5-BISPHOSPHATE ORYZA SATIVA JAPONICA GROUP RUBISCO PHOTOSYNTHESIS ALPHA/BETA BARREL N-METHYLMETHIONITRANSLATIONAL MODIFICATION LYASE
Ref.: CRYSTAL STRUCTURE OF RICE RUBISCO AND IMPLICATIONS ACTIVATION INDUCED BY POSITIVE EFFECTORS NADPH AND 6-PHOSPHOGLUCONATE J.MOL.BIOL. V. 422 75 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 1WDD - CAP C6 H14 O13 P2 C([C@H]([C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1WDD - CAP C6 H14 O13 P2 C([C@H]([C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1WDD - CAP C6 H14 O13 P2 C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CAP; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 CAP 1 1
2 XDP 0.543478 0.945946
3 DER 0.434783 0.918919
4 DEZ 0.434783 0.918919
5 4TP 0.416667 0.772727
6 PA5 0.408163 0.918919
7 R10 0.408163 0.918919
8 HG3 0.404762 0.810811
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DQX BMP 0.003618 0.40612 2.99625
2 2Q8Z NUP 0.0018 0.4075 3.125
3 1TRD PGH 0.007253 0.41622 3.2
4 5FYR INS 0.0116 0.4196 3.90625
5 2FLI DX5 0.004683 0.40613 3.90625
6 4ORM FMN 0.01575 0.42257 3.99003
7 4ORM 2V6 0.01575 0.42257 3.99003
8 4ORM ORO 0.01575 0.42257 3.99003
9 3CTL S6P 0.005828 0.40211 4.329
10 5DYO FLU 0.01992 0.41192 4.6875
11 3VKC FPQ 0.004003 0.40312 4.6875
12 2YPI PGA 0.004052 0.43276 4.8583
13 1M5W DXP 0.0235 0.40364 4.93827
14 4NAE 1GP 0.000233 0.51574 5.46875
15 4UTU LRY 0.002184 0.43631 5.46875
16 5A1S FLC 0.00678 0.43391 5.46875
17 4UTW RFW 0.003245 0.42419 5.46875
18 5EYW PGA 0.01523 0.40893 5.46875
19 3OPT AKG 0.03049 0.40033 5.63003
20 1SW0 PGA 0.002949 0.43473 5.64516
21 3OVR 5SP 0.0009445 0.42304 5.70175
22 2BTM PGA 0.01292 0.4125 5.95238
23 2F6U CIT 0.01166 0.41931 5.98291
24 3EXS 5RP 0.0005652 0.47424 6.33484
25 1QDS PGA 0.003591 0.43531 6.3745
26 2ZZV LAC 0.01809 0.4122 6.92521
27 2NSX IFM 0.003953 0.42871 7.03125
28 4BI7 PGA 0.008658 0.42118 7.03125
29 5TCI MLI 0.01354 0.41812 7.03125
30 4YMZ 13P 0.01148 0.41507 7.03125
31 4CFU 2WC 0.01568 0.4003 7.03125
32 4I9A NCN 0.002097 0.42862 7.63889
33 1Q6O LG6 0.0009395 0.4485 7.8125
34 4AF0 IMP 0.001012 0.43821 9.375
35 2BLE 5GP 0.003212 0.42469 9.375
36 3AI3 SOE 0.01872 0.40874 9.375
37 3B0P FMN 0.002672 0.428 10.1562
38 4NRT 2NG 0.01039 0.4162 10.1562
39 1W3T 3GR 0.001328 0.45562 10.2041
40 4LOC OXM 0.01596 0.40102 10.9375
41 4JEJ 1GP 0.0004459 0.47354 11.0656
42 1VKF CIT 0.01625 0.41461 11.1702
43 2VSU V55 0.01035 0.41731 11.7188
44 3GLC R5P 0.01223 0.40543 13.2812
45 2C6Q IMP 0.001825 0.40229 13.2812
46 1VPD TLA 0.01594 0.40641 13.7124
47 4IXH IMP 0.002577 0.4016 14.0625
48 3WIR BGC 0.01889 0.41009 14.8438
49 4EWN 0VR 0.005564 0.4136 15.0198
50 3QH2 3NM 0.002441 0.45406 15.625
51 1FEC FAD 0.01476 0.41397 17.9688
52 4HKP 16B 0.002458 0.42169 25.7812
53 3MI2 PFU 0.01136 0.42013 25.7812
54 2QCD U5P 0.002498 0.41769 25.7812
55 4HKP TKW 0.003541 0.40194 25.7812
56 4PTN GXV 0.01171 0.42078 28.9062
57 4BXF AKG 0.01905 0.40983 31.5789
58 2OEM 1AE 0.000005457 0.49687 42.1307
Pocket No.: 2; Query (leader) PDB : 1WDD; Ligand: CAP; 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: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1WDD; Ligand: CAP; 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: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1WDD; Ligand: CAP; 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: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1WDD; Ligand: CAP; 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: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback