Receptor
PDB id Resolution Class Description Source Keywords
3KDN 2.09 Å EC: 4.1.1.39 CRYSTAL STRUCTURE OF TYPE III RUBISCO SP4 MUTANT COMPLEXED W THERMOCOCCUS KODAKARAENSIS RIBULOSE-15-BISPHOSPHATE CARBOXYLASE/OXYGENASE RUBISCO CADIOXIDE FIXATION LYASE MAGNESIUM METAL-BINDING MONOOXYG
Ref.: STRUCTURE-BASED CATALYTIC OPTIMIZATION OF A TYPE II FROM A HYPERTHERMOPHILE J.BIOL.CHEM. V. 285 39339 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CAP A:600;
B:600;
C:600;
D:600;
E:600;
F:600;
G:600;
H:600;
I:600;
J:600;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
356.115 C6 H14 O13 P2 C([C@...
MG A:500;
B:500;
C:500;
D:500;
E:500;
F:500;
G:500;
H:500;
I:500;
J:500;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KDN 2.09 Å EC: 4.1.1.39 CRYSTAL STRUCTURE OF TYPE III RUBISCO SP4 MUTANT COMPLEXED W THERMOCOCCUS KODAKARAENSIS RIBULOSE-15-BISPHOSPHATE CARBOXYLASE/OXYGENASE RUBISCO CADIOXIDE FIXATION LYASE MAGNESIUM METAL-BINDING MONOOXYG
Ref.: STRUCTURE-BASED CATALYTIC OPTIMIZATION OF A TYPE II FROM A HYPERTHERMOPHILE J.BIOL.CHEM. V. 285 39339 2010
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3A12 - CAP C6 H14 O13 P2 C([C@H]([C....
2 3KDO - CAP C6 H14 O13 P2 C([C@H]([C....
3 3KDN - CAP C6 H14 O13 P2 C([C@H]([C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 3A12 - CAP C6 H14 O13 P2 C([C@H]([C....
2 3KDO - CAP C6 H14 O13 P2 C([C@H]([C....
3 3KDN - CAP C6 H14 O13 P2 C([C@H]([C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 3A12 - CAP C6 H14 O13 P2 C([C@H]([C....
2 3KDO - CAP C6 H14 O13 P2 C([C@H]([C....
3 3KDN - 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 : 3KDN; Ligand: CAP; 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: 3kdn.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3KDN; Ligand: CAP; Similar sites found: 63
This union binding pocket(no: 2) in the query (biounit: 3kdn.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q3O FMN 0.008884 0.41835 1.53453
2 5BRP PNG 0.04118 0.41403 2.02703
3 2CJA ATP 0.0248 0.41214 2.02703
4 3B9O FMN 0.02634 0.40778 2.04545
5 1DQX BMP 0.005512 0.4308 2.24719
6 2FFC U5P 0.007847 0.43009 2.26629
7 4UWH JXM 0.02654 0.41388 2.47748
8 4NAE 1GP 0.0008322 0.51701 2.66667
9 4RT1 C2E 0.03609 0.40395 2.67857
10 5A1S FLC 0.009142 0.45711 2.7027
11 1SW0 PGA 0.0006449 0.50093 2.82258
12 3CTL S6P 0.01626 0.41199 3.0303
13 3GLC R5P 0.01716 0.42715 3.05085
14 3VKC FPQ 0.005227 0.43185 3.14685
15 4WZH FMN 0.009513 0.40899 3.17003
16 1TRD PGH 0.001913 0.47654 3.2
17 5C2F JTH 0.03954 0.41466 3.59712
18 2YPI PGA 0.0008623 0.49977 3.64372
19 1EIX BMQ 0.009712 0.42898 3.67347
20 2QCD U5P 0.003223 0.44492 3.84615
21 3OVR 5SP 0.00116 0.45819 3.94737
22 1QDS PGA 0.0007293 0.50361 3.98406
23 4IXH IMP 0.01257 0.40884 4.15512
24 1W3T 3GR 0.01444 0.4221 4.42177
25 2Z6I FMN 0.003592 0.43608 4.51807
26 1Z44 FMN 0.01732 0.42335 4.73373
27 1Z48 FMN 0.01765 0.41953 4.73373
28 1Z41 FMN 0.01831 0.41874 4.73373
29 4HKP 16B 0.004276 0.44266 4.80769
30 4HKP TKW 0.007196 0.42248 4.80769
31 1LYX PGA 0.002795 0.46354 4.83871
32 4BI7 PGA 0.002241 0.48302 5.05837
33 3JUC PCA 0.04034 0.41676 5.22876
34 1II7 DA 0.04658 0.41003 5.40541
35 5EYW PGA 0.0016 0.49094 5.62249
36 2Q8Z NUP 0.006316 0.42212 5.84795
37 2XG5 EC2 0.04343 0.42127 5.9633
38 2XG5 EC5 0.04343 0.42127 5.9633
39 3EXS 5RP 0.00005957 0.56107 6.33484
40 4UTU LRY 0.0007398 0.49273 6.55022
41 4UTW RFW 0.001149 0.47842 6.55022
42 2C6Q IMP 0.01538 0.40245 6.55271
43 4YMZ 13P 0.001505 0.49237 6.77291
44 1VKF CIT 0.02317 0.42799 6.91489
45 2BKX F6R 0.0417 0.40379 7.02479
46 2BTM PGA 0.001568 0.49141 7.14286
47 4I9A NCN 0.01355 0.42192 7.29167
48 3B0P FMN 0.001698 0.47002 7.42857
49 5TCI MLI 0.00146 0.50005 7.80488
50 1DBT U5P 0.006786 0.4331 7.94979
51 2Q8E OGA 0.04832 0.4165 7.95455
52 2FLI DX5 0.00572 0.43006 8.63636
53 1TV5 FMN 0.00851 0.40855 8.80361
54 1M5W DXP 0.0345 0.42239 9.87654
55 3QH2 3NM 0.002425 0.48665 9.95475
56 5CSS G3P 0.04561 0.41176 11.0619
57 2F6U CIT 0.004222 0.4733 11.1111
58 5VIT MLI 0.02282 0.41528 11.1111
59 4JEJ 1GP 0.0003734 0.51319 12.2951
60 1W8S FBP 0.0335 0.40869 12.5475
61 1Q6O LG6 0.0002817 0.50865 13.8889
62 4EWN 0VR 0.008692 0.43485 17.3913
63 1O4T OXL 0.0215 0.42467 18.0451
Pocket No.: 3; Query (leader) PDB : 3KDN; 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: 3kdn.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3KDN; 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: 3kdn.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3KDN; 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: 3kdn.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3KDN; 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: 3kdn.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3KDN; 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: 3kdn.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3KDN; 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: 3kdn.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 3KDN; Ligand: CAP; 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: 3kdn.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 3KDN; Ligand: CAP; 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: 3kdn.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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