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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: 93
This union binding pocket(no: 1) in the query (biounit: 3k8d.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 5WHU SIA 1.51515
2 5WHU SIA GAL GLC 1.51515
3 1FLJ GSH 1.53846
4 6F68 4EU 1.62602
5 6F68 GSH 1.62602
6 3OV6 MK0 1.89394
7 3WLV AZA 2.27273
8 1SDW IYT 2.27273
9 1YIQ PQQ 2.27273
10 6HOY TSN 2.65152
11 2QEN ADP 2.65152
12 2WPB ZZI 2.65152
13 5WA0 MSS 2.65152
14 4HMT FMN 2.66667
15 2RHW C0E 3.0303
16 5LXT ACP 3.4965
17 5ZCT ANP 3.78788
18 2YPO PHE 3.78788
19 4IMG NGF 3.78788
20 1U59 STU 3.78788
21 4NBW NAD 3.89105
22 4Q5M ROC 3.94089
23 1S7G APR 3.95257
24 1S7G NAD 3.95257
25 1YRO GDU 4.06504
26 1Z4O GL1 4.0724
27 4MFZ MFK 4.16667
28 5CX6 CDP 4.16667
29 6AMI TRP 4.16667
30 2HK9 SKM 4.16667
31 4JD0 1KH 4.38247
32 3KYG 5GP 5GP 4.40529
33 3RIY NAD 4.54545
34 2I7C AAT 4.54545
35 6G09 BXP 4.54545
36 5X7Q GLC GLC GLC 4.54545
37 5JGA 6KC 4.54545
38 3VC1 SAH 4.80769
39 3VC1 GST 4.80769
40 4JD3 PLM 4.92424
41 4JD3 COA 4.92424
42 1VAY AZA 4.92424
43 5XFV FMN 4.92424
44 6HQD SRT 5.30303
45 2MAS PIR 5.30303
46 1I7L ATP 5.30303
47 5K2M ADP 5.66038
48 3AB1 FAD 5.68182
49 2R40 EPH 5.70342
50 2BKX F6R 5.78512
51 1T36 ADP 6.02094
52 3HRD FAD 6.06061
53 5EJL C2E 6.45161
54 1C9K 5GP 6.66667
55 5SWI BMA 6.81818
56 3VPD CIT 6.81818
57 1V97 FAD 7.19697
58 3NRZ FAD 7.19697
59 1FIQ FAD 7.19697
60 1V97 MTE 7.19697
61 3HNC TTP 7.19697
62 3NRZ HPA 7.19697
63 4YSW NAI 7.57576
64 4YSW FAD 7.57576
65 1N2X SAM 7.57576
66 2IMF GSH 7.88177
67 2IMF TOM 7.88177
68 1H5T DAU 7.95455
69 1H5R G1P 7.95455
70 5T2Z 017 8.08081
71 5XK9 DMA 8.18966
72 5XK9 GST 8.18966
73 1IIM TTP 8.33333
74 5GM1 SAH 8.33333
75 3T50 FMN 8.59375
76 3KV8 FAH 8.63309
77 2AZC 3TL 9.09091
78 3MKN DNB 9.4697
79 4P86 5GP 10.3825
80 1FNN ADP 10.6061
81 4A59 AMP 10.9848
82 2PA4 UPG 11.3636
83 5MZY 8EZ 11.3636
84 1I9G SAM 13.2576
85 4BJ8 BTN 13.4921
86 1N62 MCN 13.5417
87 3H5N ATP 14.0152
88 3JUK UPG 15.1515
89 1T3Q MCN 16.6667
90 1IDA 0PO 17.1717
91 3VPB ADP 21.5909
92 3VPC ADP 21.5909
93 1HV9 UD1 22.3485
Pocket No.: 2; Query (leader) PDB : 3K8D; Ligand: KDO; Similar sites found with APoc: 16
This union binding pocket(no: 2) in the query (biounit: 3k8d.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1KSK URA 2.13675
2 3FV3 IVA VAL VAL STA ALA STA 3.0303
3 4XF6 ADP 3.40909
4 4XF6 INS 3.40909
5 4XF6 LIP 3.40909
6 3U2U UDP 3.42205
7 2IV2 MGD 3.78788
8 3VYW SAM 3.78788
9 3S5W FAD 4.54545
10 3HRD MCN 6.06061
11 4PW9 MSS 6.60377
12 1F8Y 5MD 7.64331
13 2FLI DX5 7.72727
14 3C3N FMN 9.4697
15 3O9L LPN 10.241
16 2HGS ADP 15.1515
Pocket No.: 3; Query (leader) PDB : 3K8D; Ligand: CTP; Similar sites found with APoc: 66
This union binding pocket(no: 3) in the query (biounit: 3k8d.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5DQY BEZ None
2 5VCM UDP 1.13636
3 3CKJ CIT 1.89394
4 3KRU FMN 1.89394
5 5TZJ UD1 2.27273
6 4DHY GLC 2.27273
7 1V84 UDP 2.37154
8 3NOJ PYR 2.94118
9 5JBE MAL 3.0303
10 3E9I XAH 3.0303
11 3DR4 G4M 3.0303
12 2BGS NDP 3.0303
13 3ZF8 GDP 3.40909
14 1ONI BEZ 3.62319
15 1LVW TYD 3.78788
16 2ICY UPG 3.78788
17 1JV1 UD1 3.78788
18 1EK6 UPG 3.78788
19 3LL5 IP8 4.01606
20 1G51 AMO 4.16667
21 1I52 CTP 4.23729
22 1TKE SER 4.46429
23 2BO4 FLC 4.54545
24 2APC UDM 4.92424
25 3CU0 UDP 5.68182
26 3CU0 GAL GAL SO4 5.68182
27 1QNF HDF 6.06061
28 2YQS UD1 6.43939
29 4ONA UW1 6.43939
30 4DEC 3PG 6.81818
31 4DEC UDP 6.81818
32 1O7Q UDP 6.81818
33 1O7Q GAL NAG 6.81818
34 4HA6 FAD 6.81818
35 4AVV CD 6.86275
36 4UZI IMD 7.57576
37 1H5T DAU 7.95455
38 1H5S TMP 7.95455
39 1H5R THM 7.95455
40 1WVC CTP 8.10811
41 5XK9 DMA 8.18966
42 1IIM TTP 8.33333
43 2OEG UPG 8.33333
44 3B8X G4M 8.33333
45 4CT7 TRP 8.64198
46 3EWC MCF 9.09091
47 2J0B UDP 9.4697
48 1EQ2 NAP 9.84848
49 4Y7U 2KH 9.95671
50 3KJS NAP 10.2273
51 2PA4 UPG 11.3636
52 1W55 C 11.3636
53 4LED XXR 11.3636
54 1FRW GTP 11.8557
55 6H21 UD1 12.5
56 6C9B EGV 12.5
57 2YC5 6BC 13.1579
58 1T57 FMN 13.5922
59 3JUK UPG 15.1515
60 1EYR CDP 16.2281
61 1XXA ARG 17.9487
62 2YOA SEP 21.0526
63 1HV9 UD1 22.3485
64 2XWL CTP 24.2152
65 4KQL 1SG 24.6212
66 5HS2 CTP 27.1552
Pocket No.: 4; Query (leader) PDB : 3K8D; Ligand: CTP; Similar sites found with APoc: 15
This union binding pocket(no: 4) in the query (biounit: 3k8d.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4K7O EKZ 2.97619
2 5NM7 GLY 4.16667
3 2I4O ATP 4.16667
4 5UR0 NAD 4.16667
5 3GDN FAD 4.16667
6 5LUB 3Y7 4.19847
7 2A9G ARG 4.54545
8 4XQC NAD 4.54545
9 5FJJ MAN 4.92424
10 3MF2 AMP 5.30303
11 3RG9 WRA 5.83333
12 2J3M ATP 6.81818
13 2J3M PRI 6.81818
14 4DV8 0LX 7.95455
15 5XK9 GST 8.18966
Pocket No.: 5; Query (leader) PDB : 3K8D; Ligand: KDO; Similar sites found with APoc: 2
This union binding pocket(no: 5) in the query (biounit: 3k8d.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4YZC STU 4.16667
2 5K5Z ANP 6.43939
Pocket No.: 6; Query (leader) PDB : 3K8D; Ligand: KDO; Similar sites found with APoc: 3
This union binding pocket(no: 6) in the query (biounit: 3k8d.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4CW5 FMN 2.27273
2 5X7Q GLC GLC GLC GLC 4.54545
3 2A9D MTE 4.54545
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: 2
This union binding pocket(no: 8) in the query (biounit: 3k8d.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5GWT SIN 4.16667
2 3W9F I3P 9.23077
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