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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 19 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 with APoc: 120
This union binding pocket(no: 1) in the query (biounit: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2IRY DGT 2.34375
2 1ME8 RVP 2.51572
3 2Z6I FMN 2.71084
4 1DQX BMP 2.99625
5 2Q8Z NUP 3.125
6 1TRD PGH 3.2
7 2CJA ATP 3.90625
8 1UUO FMN 3.90625
9 1UUO BRF 3.90625
10 1UUO ORO 3.90625
11 1TV5 FMN 3.90625
12 5FYR INS 3.90625
13 2FLI DX5 3.90625
14 2Z6J FMN 3.91566
15 1PVN MZP 3.98936
16 3CTL S6P 4.329
17 2Q3O FMN 4.34783
18 3CEV ARG 4.6875
19 5DYO FLU 4.6875
20 3VKC FPQ 4.6875
21 5A5W GUO 4.74308
22 5I34 GDP 4.7619
23 2YPI PGA 4.8583
24 1M5W DXP 4.93827
25 1ONI BEZ 5.07246
26 4NAE 1GP 5.46875
27 4UTU LRY 5.46875
28 5A1S FLC 5.46875
29 4UTW RFW 5.46875
30 5EYW PGA 5.46875
31 3OPT AKG 5.63003
32 1SW0 PGA 5.64516
33 1OX5 1PR 5.66038
34 3OVR 5SP 5.70175
35 3WUC GLC GAL 5.83942
36 2BTM PGA 5.95238
37 2F6U CIT 5.98291
38 5XFV FMN 5.98802
39 1OYB FMN 6.07966
40 1OYB HBA 6.07966
41 2Y88 2ER 6.14754
42 3KIH GDL 6.18557
43 1OVD ORO 6.25
44 1OVD FMN 6.25
45 3Q9T FAY 6.25
46 5LIA 6XN 6.25
47 3BW2 FMN 6.25
48 6BKA FMN 6.25
49 2NU8 COA 6.25
50 1OFD FMN 6.25
51 3EXS 5RP 6.33484
52 1QDS PGA 6.3745
53 4IGH 1EA 6.72043
54 4IGH ORO 6.72043
55 4IGH FMN 6.72043
56 2ZZV LAC 6.92521
57 5TCI MLI 7.03125
58 2NSX IFM 7.03125
59 5W75 SUC 7.03125
60 4BI7 PGA 7.03125
61 4YMZ 13P 7.03125
62 2Y0I AKG 7.03125
63 1JCM 137 7.03125
64 4CFU 2WC 7.03125
65 2BPM 529 7.03125
66 2TPS TPS 7.04846
67 4I9A NCN 7.63889
68 1Q6O LG6 7.8125
69 6BVE PGA 7.8125
70 2D3S TNR 8.59375
71 4Q4K FMN 8.59375
72 4WZH FMN 8.93372
73 1EP2 ORO 9.00322
74 1EP2 FMN 9.00322
75 4AF0 IMP 9.375
76 2BLE 5GP 9.375
77 1GTE IUR 9.375
78 1GTE FMN 9.375
79 3AI3 SOE 9.375
80 1RJW ETF 9.375
81 1CX9 NHP 9.375
82 3MJY FMN 9.53757
83 3MJY IJZ 9.53757
84 1LBF 137 9.7166
85 4Z0G 5GP 10.1562
86 4Z87 5GP 10.1562
87 3B0P FMN 10.1562
88 4NRT 2NG 10.1562
89 3C3N FMN 10.1562
90 1W3T 3GR 10.2041
91 4LOC OXM 10.9375
92 4JEJ 1GP 11.0656
93 1VKF CIT 11.1702
94 2VSS V55 11.7188
95 2VSU V55 11.7188
96 5J5R IMP 12.5964
97 5J5R 6G1 12.5964
98 1LYX PGA 12.9032
99 2C6Q NDP 13.2812
100 2C6Q IMP 13.2812
101 3GLC R5P 13.2812
102 3TAO PGH 14.0625
103 4IXH IMP 14.0625
104 3WIR BGC 14.8438
105 4EWN 0VR 15.0198
106 5O2Z FLC 15.126
107 3QH2 3NM 15.625
108 3O75 F1X 15.625
109 1FEC FAD 17.9688
110 4TMC FMN 17.9688
111 5AHN IMP 19.5312
112 2HSA FMN 20.3125
113 1MLD CIT 21.0938
114 3MI2 PFU 25.7812
115 2QCD U5P 25.7812
116 4HKP TKW 25.7812
117 4HKP 16B 25.7812
118 4PTN GXV 28.9062
119 4BXF AKG 31.5789
120 2OEM 1AE 42.1307
Pocket No.: 2; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1WDD; Ligand: CAP; 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: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found with APoc: 17
This union binding pocket(no: 5) in the query (biounit: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1GQ2 OXL 3.14465
2 4TQK NAG 3.90625
3 4ORM 2V6 3.99003
4 4ORM FMN 3.99003
5 4ORM ORO 3.99003
6 2PEL LBT 4.66102
7 2O66 FLC 5.46875
8 4UWH JXM 7.54717
9 2RI1 GLP 7.8125
10 2WZF BGC 7.8125
11 4UP4 GAL NAG 8.59375
12 2J5B TYE 10.9375
13 1EIX BMQ 11.0204
14 5BJX UDP 11.7188
15 5BJX NAD 11.7188
16 3BJE URA 14.0625
17 1ICP FMN 14.8438
Pocket No.: 6; Query (leader) PDB : 1WDD; Ligand: CAP; 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: 1wdd.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1WDD; Ligand: CAP; Similar sites found with APoc: 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 Sequence Similarity
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