Receptor
PDB id Resolution Class Description Source Keywords
2VDH 2.3 Å EC: 4.1.1.39 CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT C172S MUTATION CHLAMYDOMONAS REINHARDTII VICINAL CYSTEINES CO2/O2 SPECIFICITY PHOTOSYNTHESIS TRANSIT PEPTIDE PHOTORESPIRATION METAL-BINDING HYDROXYLATION OXIDOREDUCTASE METHYLATION CHLOROPLAST CALVIN CYCLE MONOOXYGENASE LYASE RUBISCO PLASTID MAGNESIUM ACETYLATION CARBON DIOXIDE FIXATION
Ref.: STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF THE REPLACEMENT OF PROXIMAL RESIDUES CYS-172 AND CYS-192 IN THE LARGE SUBUNIT OF RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE FROM CHLAMYDOMONAS REINHARDTII BIOCHEM.J. V. 411 241 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CAP A:1477;
B:1477;
C:1477;
D:1477;
E:1477;
F:1477;
G:1477;
H:1477;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
356.115 C6 H14 O13 P2 C([C@...
EDO A:1478;
A:1479;
A:1480;
A:1481;
A:1482;
A:1483;
B:1478;
B:1479;
B:1480;
B:1481;
B:1482;
C:1478;
C:1479;
C:1480;
C:1481;
C:1482;
C:1483;
D:1478;
D:1479;
D:1480;
D:1481;
D:1482;
E:1478;
E:1479;
E:1480;
E:1481;
E:1482;
E:1483;
F:1478;
F:1479;
F:1480;
F:1481;
F:1482;
F:1483;
G:1478;
G:1479;
G:1480;
G:1481;
G:1482;
H:1478;
H:1479;
H:1480;
H:1481;
H:1482;
H:1483;
I:1141;
J:1141;
J:1142;
K:1141;
K:1142;
L:1141;
M:1141;
M:1142;
N:1141;
N:1142;
O:1141;
O:1142;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MG A:1476;
B:1476;
C:1476;
D:1476;
E:1476;
F:1476;
G:1476;
H:1476;
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;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VDH 2.3 Å EC: 4.1.1.39 CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT C172S MUTATION CHLAMYDOMONAS REINHARDTII VICINAL CYSTEINES CO2/O2 SPECIFICITY PHOTOSYNTHESIS TRANSIT PEPTIDE PHOTORESPIRATION METAL-BINDING HYDROXYLATION OXIDOREDUCTASE METHYLATION CHLOROPLAST CALVIN CYCLE MONOOXYGENASE LYASE RUBISCO PLASTID MAGNESIUM ACETYLATION CARBON DIOXIDE FIXATION
Ref.: STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF THE REPLACEMENT OF PROXIMAL RESIDUES CYS-172 AND CYS-192 IN THE LARGE SUBUNIT OF RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE FROM CHLAMYDOMONAS REINHARDTII BIOCHEM.J. V. 411 241 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2VDH - 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 2VDH - 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 2VDH - 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 : 2VDH; Ligand: CAP; Similar sites found: 60
This union binding pocket(no: 1) in the query (biounit: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2C6Q IMP 0.001838 0.40557 2.85714
2 1SW0 PGA 0.002364 0.44118 3.22581
3 3WIR BGC 0.01891 0.41167 3.57143
4 3OPT AKG 0.03188 0.40088 3.57143
5 2ZZV LAC 0.03005 0.40025 3.57143
6 1W3T 3GR 0.001337 0.45385 4.28571
7 4HKP 16B 0.001352 0.43487 4.28571
8 3MI2 PFU 0.007613 0.42519 4.28571
9 4ORM 2V6 0.01717 0.41794 4.28571
10 4ORM ORO 0.01717 0.41794 4.28571
11 4ORM FMN 0.01717 0.41794 4.28571
12 4HKP TKW 0.002081 0.41418 4.28571
13 2Q8Z NUP 0.001881 0.41075 4.28571
14 1YXM ADE 0.02685 0.40427 4.29043
15 2QCD U5P 0.001612 0.42018 4.61538
16 4I9A NCN 0.002261 0.42907 5
17 4UTW RFW 0.00332 0.42561 5
18 4YMZ 13P 0.008457 0.42345 5
19 5EYW PGA 0.0119 0.41601 5
20 2FLI DX5 0.004738 0.40446 5
21 2YPI PGA 0.003897 0.43543 5.26316
22 4IXH IMP 0.003225 0.40146 5.54017
23 4IGH 1EA 0.02056 0.41482 5.64516
24 4IGH ORO 0.02056 0.41482 5.64516
25 4IGH FMN 0.02056 0.41482 5.64516
26 3Q9T FAY 0.01064 0.41038 5.71429
27 1M5W DXP 0.008648 0.42772 5.76132
28 2XG5 EC2 0.03054 0.40024 5.78035
29 2XG5 EC5 0.03054 0.40024 5.78035
30 2BTM PGA 0.009336 0.4213 5.95238
31 3AI3 SOE 0.01965 0.40932 6.08365
32 5A5W GUO 0.002903 0.43675 6.42857
33 4UTU LRY 0.002899 0.4325 6.42857
34 3OVR 5SP 0.0009528 0.4278 6.42857
35 1DQX BMP 0.002746 0.41435 6.42857
36 1QDS PGA 0.002696 0.44324 7.14286
37 2F6U CIT 0.01432 0.41643 7.14286
38 4EWN 0VR 0.006244 0.41313 7.14286
39 4AF0 IMP 0.001219 0.43095 7.85714
40 3B0P FMN 0.002863 0.42853 7.85714
41 1Q6O LG6 0.0005587 0.42425 7.87037
42 3VKC FPQ 0.005219 0.4027 8.04196
43 3EXS 5RP 0.0006099 0.47469 8.57143
44 3T7V MD0 0.006815 0.43304 8.57143
45 4CFU 2WC 0.01577 0.40188 9.16031
46 5TVM PUT 0.02695 0.40488 9.41177
47 2WZF BGC 0.02049 0.40848 10
48 2TPS TPS 0.005926 0.40689 10.5727
49 2Y88 2ER 0.004622 0.42334 10.6557
50 2NSX IFM 0.004086 0.42987 10.7143
51 5TCI MLI 0.01423 0.4191 10.7143
52 3MJY FMN 0.007388 0.41082 11.4286
53 3MJY IJZ 0.007388 0.41082 11.4286
54 4JEJ 1GP 0.000472 0.40995 11.4754
55 2BLE 5GP 0.005475 0.41127 14.2857
56 3GLC R5P 0.01178 0.40793 14.2857
57 4UWH JXM 0.003954 0.42624 15
58 3QH2 3NM 0.002129 0.45901 16.4286
59 4NAE 1GP 0.0001835 0.52332 21.4286
60 2OEM 1AE 0.000002925 0.49735 41.1622
Pocket No.: 2; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2VDH; 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: 2vdh.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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