Receptor
PDB id Resolution Class Description Source Keywords
3K8D 1.9 Å EC: 2.7.7.38 CRYSTAL STRUCTURE OF E. COLI LIPOPOLYSACCHARIDE SPECIFIC CMP SYNTHETASE IN COMPLEX WITH CTP AND 2-DEOXY-KDO ESCHERICHIA COLI KDSB SYNTHETASE KDO COMPLEX LIPOPOLYSACCHARIDE BIOSYNTHESISMAGNESIUM NUCLEOTIDYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURE-BASED MECHANISM OF CMP-2-KETO-3-DEOXYMANNO-OCTULONIC ACID SYNTHETASE: CONVERGENT EVOLUTION OF A SUGAR-ACTIVATING ENZYME W DNA/RNA POLYMERASES J.BIOL.CHEM. V. 284 35514 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CTP A:1243;
B:1243;
C:1243;
D:1243;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
KDO A:1244;
B:1244;
C:1244;
D:1244;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 1.7 uM
238.192 C8 H14 O8 C1[C@...
MG A:1242;
B:1242;
C:1242;
D:1242;
Invalid;
Invalid;
Invalid;
Invalid;
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
3K8D 1.9 Å EC: 2.7.7.38 CRYSTAL STRUCTURE OF E. COLI LIPOPOLYSACCHARIDE SPECIFIC CMP SYNTHETASE IN COMPLEX WITH CTP AND 2-DEOXY-KDO ESCHERICHIA COLI KDSB SYNTHETASE KDO COMPLEX LIPOPOLYSACCHARIDE BIOSYNTHESISMAGNESIUM NUCLEOTIDYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURE-BASED MECHANISM OF CMP-2-KETO-3-DEOXYMANNO-OCTULONIC ACID SYNTHETASE: CONVERGENT EVOLUTION OF A SUGAR-ACTIVATING ENZYME W DNA/RNA POLYMERASES J.BIOL.CHEM. V. 284 35514 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3K8D Kd = 1.7 uM KDO C8 H14 O8 C1[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 4 families.
1 3K8D Kd = 1.7 uM KDO C8 H14 O8 C1[C@H]([C....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2Y6P - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 3K8D Kd = 1.7 uM KDO C8 H14 O8 C1[C@H]([C....
3 1H7G - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
4 1H7T - C5P SIA n/a n/a
5 1H7F - C5P C9 H14 N3 O8 P C1=CN(C(=O....
6 1H7H - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CTP; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 CTP 1 1
2 HF4 1 1
3 CDP 0.895522 1
4 CAR 0.753623 0.985507
5 C 0.753623 0.985507
6 C5P 0.753623 0.985507
7 7XL 0.74026 0.944444
8 C2G 0.734177 0.957747
9 C5G 0.702381 0.944444
10 CDM 0.690476 0.894737
11 CDC 0.678571 0.82716
12 CXY 0.674419 0.944444
13 UTP 0.620253 0.942029
14 1AA 0.617021 0.906667
15 DCP 0.609756 0.90411
16 AR3 0.608696 0.857143
17 CTN 0.608696 0.857143
18 GTF 0.595238 0.90411
19 C C C C 0.58427 0.916667
20 91P 0.582524 0.851852
21 I5A 0.577465 0.816901
22 C C 0.568182 0.929577
23 UDP 0.54321 0.942029
24 MCN 0.542056 0.819277
25 2AA 0.542056 0.693878
26 C3P 0.538462 0.942857
27 PMT 0.52381 0.85
28 YYY 0.52381 0.90411
29 GCQ 0.523256 0.90411
30 CSQ 0.520408 0.905405
31 CSV 0.520408 0.905405
32 16B 0.518519 0.917808
33 PCD 0.517544 0.781609
34 C2P 0.5 0.957143
35 GPC 0.495575 0.819277
36 FN5 0.495413 0.871795
37 CSF 0.491071 0.871795
38 DKZ 0.481013 0.746667
39 8GT 0.473118 0.907895
40 UNP 0.47191 0.915493
41 TKW 0.46988 0.971429
42 H6Y 0.463158 0.855263
43 5HM 0.458824 0.958333
44 G C 0.45614 0.8375
45 MGT 0.453608 0.829268
46 UPP 0.452632 0.888889
47 UDH 0.452632 0.844156
48 GUD 0.447917 0.888889
49 UPG 0.447917 0.888889
50 UFM 0.447917 0.888889
51 GDU 0.447917 0.888889
52 DCM 0.447059 0.890411
53 DC 0.447059 0.890411
54 A C A C 0.440678 0.835443
55 UPF 0.434343 0.842105
56 UFG 0.434343 0.842105
57 U2F 0.434343 0.842105
58 U5P 0.433735 0.927536
59 U 0.433735 0.927536
60 660 0.43299 0.876712
61 URM 0.43299 0.876712
62 UP5 0.432432 0.857143
63 5GW 0.431579 0.890411
64 UPU 0.430108 0.887324
65 U A C C 0.428571 0.846154
66 PRT 0.424528 0.842105
67 C5P SIA 0.423729 0.893333
68 DOC 0.423529 0.890411
69 G3N 0.421569 0.890411
70 G G G C 0.421488 0.85
71 G8D 0.421053 0.907895
72 UDX 0.42 0.888889
73 UAD 0.42 0.888889
74 A G C C 0.418033 0.848101
75 2KH 0.417582 0.915493
76 3UC 0.417476 0.842105
77 4GW 0.415842 0.866667
78 UGB 0.411765 0.901408
79 V12 0.411765 0.75
80 USQ 0.411765 0.780488
81 UGA 0.411765 0.901408
82 CG2 0.410256 0.873418
83 GEO 0.407407 0.783784
84 G C C C 0.404762 0.860759
85 NVG 0.403846 0.731707
86 44P 0.402299 0.902778
87 8OD 0.402062 0.855263
88 A U C C 0.4 0.835443
Ligand no: 2; Ligand: KDO; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 KDO 1 1
2 KDN 0.64 0.96875
3 KDM 0.64 0.96875
4 KDE 0.467742 0.864865
5 SLB 0.435484 0.704545
6 SIA 0.435484 0.704545
7 KDF 0.428571 0.833333
8 KDO KDO KDO 0.422535 0.8
9 NGC 0.421875 0.688889
10 NGE 0.421875 0.688889
11 18D 0.409091 0.673913
12 42D 0.409091 0.645833
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3K8D; Ligand: KDO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3k8d.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3K8D; Ligand: KDO; 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: 3k8d.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3K8D; Ligand: CTP; 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: 3k8d.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3K8D; Ligand: CTP; 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: 3k8d.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3K8D; Ligand: KDO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3k8d.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3K8D; Ligand: KDO; 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: 3k8d.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3K8D; Ligand: CTP; 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: 3k8d.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3K8D; Ligand: CTP; 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: 3k8d.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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