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: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 CTP 1 1
2 CDP 0.895522 1
3 CAR 0.753623 0.985507
4 C 0.753623 0.985507
5 C5P 0.753623 0.985507
6 7XL 0.74026 0.944444
7 C2G 0.734177 0.957747
8 C5G 0.702381 0.944444
9 CDM 0.690476 0.894737
10 CDC 0.678571 0.82716
11 CXY 0.674419 0.944444
12 CDP MG 0.662338 0.90411
13 UTP 0.620253 0.942029
14 1AA 0.617021 0.906667
15 DCP 0.609756 0.90411
16 CTN 0.608696 0.857143
17 AR3 0.608696 0.857143
18 91P 0.582524 0.851852
19 I5A 0.577465 0.816901
20 C C 0.568182 0.929577
21 UDP 0.54321 0.942029
22 2AA 0.542056 0.693878
23 MCN 0.542056 0.819277
24 C3P 0.538462 0.942857
25 YYY 0.52381 0.90411
26 PMT 0.52381 0.85
27 GCQ 0.523256 0.90411
28 CSQ 0.520408 0.905405
29 CSV 0.520408 0.905405
30 16B 0.518519 0.917808
31 PCD 0.517544 0.781609
32 C2P 0.5 0.957143
33 GPC 0.495575 0.819277
34 FN5 0.495413 0.871795
35 CSF 0.491071 0.871795
36 DKZ 0.481013 0.746667
37 8GT 0.473118 0.907895
38 UNP 0.47191 0.915493
39 TKW 0.46988 0.971429
40 H6Y 0.463158 0.855263
41 5HM 0.458824 0.958333
42 G C 0.45614 0.8375
43 MGT 0.453608 0.829268
44 UDH 0.452632 0.844156
45 UPP 0.452632 0.888889
46 UFM 0.447917 0.888889
47 GDU 0.447917 0.888889
48 GUD 0.447917 0.888889
49 UPG 0.447917 0.888889
50 DCM 0.447059 0.890411
51 DC 0.447059 0.890411
52 UFG 0.434343 0.842105
53 U2F 0.434343 0.842105
54 UPF 0.434343 0.842105
55 U5P 0.433735 0.927536
56 URM 0.43299 0.876712
57 660 0.43299 0.876712
58 UP5 0.432432 0.857143
59 5GW 0.431579 0.890411
60 UPU 0.430108 0.887324
61 U A C C 0.428571 0.846154
62 C5P SIA 0.423729 0.893333
63 DOC 0.423529 0.890411
64 G3N 0.421569 0.890411
65 G G G C 0.421488 0.85
66 G8D 0.421053 0.907895
67 UDX 0.42 0.888889
68 UAD 0.42 0.888889
69 A G C C 0.418033 0.848101
70 2KH 0.417582 0.915493
71 3UC 0.417476 0.842105
72 4GW 0.415842 0.866667
73 UGA 0.411765 0.901408
74 V12 0.411765 0.75
75 UGB 0.411765 0.901408
76 USQ 0.411765 0.780488
77 CG2 0.410256 0.873418
78 GEO 0.407407 0.783784
79 G C C C 0.404762 0.860759
80 NVG 0.403846 0.731707
81 44P 0.402299 0.902778
82 8OD 0.402062 0.855263
83 A U C C 0.4 0.835443
Ligand no: 2; Ligand: KDO; Similar ligands found: 11
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 18D 0.409091 0.673913
11 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: 21
This union binding pocket(no: 1) in the query (biounit: 3k8d.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4HP0 NOJ NAG NAG NAG 0.02939 0.40742 None
2 3OV6 MK0 0.0316 0.40944 1.89394
3 3WLV AZA 0.003623 0.42643 2.27273
4 1YIQ PQQ 0.02654 0.40255 2.27273
5 2QEN ADP 0.01185 0.41524 2.65152
6 4HMT FMN 0.03613 0.40133 2.66667
7 4MFZ MFK 0.01492 0.42435 4.16667
8 2HK9 SKM 0.01357 0.40191 4.16667
9 4JD0 1KH 0.01337 0.40049 4.38247
10 3RIY NAD 0.03371 0.40792 4.54545
11 3VC1 SAH 0.03502 0.4171 4.80769
12 1VAY AZA 0.007495 0.4032 4.92424
13 5K2M ADP 0.01372 0.42059 5.66038
14 3HRD FAD 0.01614 0.43662 6.06061
15 5SWI BMA 0.001028 0.45769 6.81818
16 1FIQ FAD 0.008836 0.44383 7.19697
17 1H5R G1P 0.004078 0.40091 7.95455
18 5T2Z 017 0.03032 0.40921 8.08081
19 2PA4 UPG 0.01429 0.4279 11.3636
20 4BJ8 BTN 0.01148 0.41396 13.4921
21 1IDA 0PO 0.01053 0.44082 17.1717
Pocket No.: 2; Query (leader) PDB : 3K8D; Ligand: KDO; 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: 3k8d.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3K8D; Ligand: CTP; Similar sites found: 31
This union binding pocket(no: 3) in the query (biounit: 3k8d.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1V84 UDP 0.005134 0.4243 2.37154
2 4K7O EKZ 0.02064 0.40545 2.97619
3 5JBE MAL 0.007632 0.44146 3.0303
4 3E9I XAH 0.02223 0.40112 3.0303
5 3ZF8 GDP 0.00547 0.41826 3.40909
6 2I4O ATP 0.002955 0.43094 4.16667
7 1G51 AMO 0.00987 0.41545 4.16667
8 3GDN FAD 0.03912 0.40204 4.16667
9 1I52 CTP 0.00003434 0.41823 4.23729
10 2BO4 FLC 0.009864 0.41256 4.54545
11 2A9G ARG 0.01562 0.40074 4.54545
12 5FJJ MAN 0.003561 0.42532 4.92424
13 2APC UDM 0.006032 0.4159 4.92424
14 3CU0 UDP 0.006117 0.41374 5.68182
15 3CU0 GAL GAL SO4 0.02672 0.40074 5.68182
16 4DV8 0LX 0.02274 0.40637 7.95455
17 1WVC CTP 0.000002175 0.4787 8.10811
18 2OEG UPG 0.006816 0.41858 8.33333
19 4CT7 TRP 0.001351 0.45842 8.64198
20 2J0B UDP 0.002445 0.43995 9.4697
21 4Y7U 2KH 0.00006929 0.41866 9.95671
22 2PA4 UPG 0.002435 0.44878 11.3636
23 4LED XXR 0.01066 0.42113 11.3636
24 1FRW GTP 0.0009473 0.43588 11.8557
25 1JYL CDC 0.0009417 0.413 14.1732
26 1EYR CDP 0.0001709 0.48271 16.2281
27 1HV9 UD1 0.00008688 0.4035 22.3485
28 4G87 UD1 0.00008827 0.40095 23.4848
29 2XWL CTP 0.00008304 0.47468 24.2152
30 4KQL 1SG 0.003231 0.45357 24.6212
31 5HS2 CTP 0.00001551 0.5274 27.1552
Pocket No.: 4; Query (leader) PDB : 3K8D; Ligand: CTP; 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: 3k8d.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3K8D; Ligand: KDO; Similar sites found: 5
This union binding pocket(no: 5) in the query (biounit: 3k8d.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3FV3 IVA VAL VAL STA ALA STA 0.03979 0.4004 3.0303
2 4YZC STU 0.03849 0.41017 4.16667
3 5K5Z ANP 0.03338 0.40037 6.43939
4 4PW9 MSS 0.007541 0.43078 6.60377
5 1C9K 5GP 0.01419 0.40273 6.66667
Pocket No.: 6; Query (leader) PDB : 3K8D; Ligand: KDO; 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: 3k8d.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3K8D; Ligand: CTP; Similar sites found: 2
This union binding pocket(no: 7) in the query (biounit: 3k8d.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CV9 VDX 0.01996 0.40339 2.91262
2 3LL5 IP8 0.0212 0.40224 4.01606
Pocket No.: 8; Query (leader) PDB : 3K8D; Ligand: CTP; 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: 3k8d.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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