Receptor
PDB id Resolution Class Description Source Keywords
1KDO 1.9 Å EC: 2.7.4.14 CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH CYTIDINE MONOPHOSPHATE ESCHERICHIA COLI NUCLEOTIDE MONOPHOSPHATE KINASE TRANSFERASE
Ref.: SUGAR SPECIFICITY OF BACTERIAL CMP KINASES AS REVEALED BY CRYSTAL STRUCTURES AND MUTAGENESIS OF ESCHERICHIA COLI ENZYME. J.MOL.BIOL. V. 315 1099 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C A:5407;
B:6407;
Valid;
Valid;
none;
none;
submit data
323.197 C9 H14 N3 O8 P C1=CN...
SO4 A:501;
A:502;
A:503;
B:601;
B:602;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KDO 1.9 Å EC: 2.7.4.14 CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH CYTIDINE MONOPHOSPHATE ESCHERICHIA COLI NUCLEOTIDE MONOPHOSPHATE KINASE TRANSFERASE
Ref.: SUGAR SPECIFICITY OF BACTERIAL CMP KINASES AS REVEALED BY CRYSTAL STRUCTURES AND MUTAGENESIS OF ESCHERICHIA COLI ENZYME. J.MOL.BIOL. V. 315 1099 2002
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2CMK - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 1KDP - C C9 H14 N3 O8 P C1=CN(C(=O....
3 1KDT - DOC C9 H14 N3 O6 P C1C[C@@H](....
4 1KDR - CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 1KDO - C C9 H14 N3 O8 P C1=CN(C(=O....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2CMK - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 1KDP - C C9 H14 N3 O8 P C1=CN(C(=O....
3 1KDT - DOC C9 H14 N3 O6 P C1C[C@@H](....
4 1KDR - CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 1KDO - C C9 H14 N3 O8 P C1=CN(C(=O....
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 2CMK - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 1KDP - C C9 H14 N3 O8 P C1=CN(C(=O....
3 1KDT - DOC C9 H14 N3 O6 P C1C[C@@H](....
4 1KDR - CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 1KDO - C C9 H14 N3 O8 P C1=CN(C(=O....
6 2H92 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 C 1 1
2 CAR 1 1
3 C5P 1 1
4 CDP 0.787879 0.985507
5 CTP 0.753623 0.985507
6 CDP MG 0.724638 0.916667
7 7XL 0.689189 0.930556
8 16B 0.676471 0.930556
9 AR3 0.672131 0.842857
10 CTN 0.672131 0.842857
11 C2G 0.662338 0.943662
12 I5A 0.634921 0.828571
13 C5G 0.634146 0.930556
14 C C 0.632911 0.942857
15 CDC 0.62963 0.8375
16 CDM 0.621951 0.881579
17 CXY 0.607143 0.930556
18 TKW 0.591549 0.985507
19 C3P 0.585714 0.956522
20 5HM 0.575342 0.944444
21 U5P 0.571429 0.941176
22 CSV 0.555556 0.917808
23 CSQ 0.555556 0.917808
24 1AA 0.554348 0.893333
25 C2P 0.541667 0.942857
26 PMT 0.540816 0.860759
27 DCM 0.540541 0.902778
28 DC 0.540541 0.902778
29 DKZ 0.521127 0.733333
30 91P 0.495146 0.839506
31 FN5 0.495146 0.858974
32 DOC 0.493333 0.902778
33 ICR 0.486842 0.861111
34 5BU 0.486842 0.876712
35 2AA 0.485714 0.683673
36 MCN 0.485714 0.807229
37 GPC 0.481481 0.829268
38 G C 0.481132 0.848101
39 5FU 0.48 0.876712
40 CSF 0.476636 0.858974
41 PCD 0.464286 0.770115
42 U A C C 0.463636 0.857143
43 C5P SIA 0.458716 0.88
44 YYY 0.451219 0.890411
45 CNU 0.45 0.915493
46 UDP 0.45 0.927536
47 44P 0.448718 0.888889
48 DCP 0.447059 0.890411
49 G G G C 0.442478 0.860759
50 A G C C 0.438596 0.858974
51 V12 0.43617 0.7375
52 NUP 0.435897 0.929577
53 GCQ 0.435294 0.890411
54 UTP 0.433735 0.927536
55 A U C C 0.429752 0.846154
56 2KH 0.428571 0.901408
57 UP6 0.428571 0.887324
58 NVG 0.427083 0.719512
59 G C C C 0.423729 0.871795
60 S5P 0.423077 0.853333
61 GEO 0.418919 0.77027
62 CH 0.417722 0.956522
63 H2U 0.415584 0.861111
64 UDP UDP 0.414634 0.898551
65 FNU 0.4125 0.88
66 JW5 0.4125 0.901408
67 8GM 0.411765 0.906667
68 DCZ 0.410959 0.77027
69 LDC 0.410959 0.77027
70 UPU 0.409091 0.9
71 BMP 0.405063 0.901408
72 BMQ 0.402597 0.885714
73 UNP 0.402299 0.901408
74 8OP 0.402299 0.853333
75 U6M 0.4 0.914286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KDO; Ligand: C; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1kdo.bio3) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KDO; Ligand: C; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 1kdo.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3B9Q MLI 0.002026 0.46828 None
2 4ZGR NGA GAL 0.02016 0.40735 1.32159
3 5GVR LMR 0.01362 0.41495 2.20264
4 4CJN QNZ 0.01855 0.41397 2.20264
5 2P3V SRT 0.01592 0.41654 3.0837
6 3FIU POP 0.01851 0.41122 3.0837
7 2VOH CIT 0.01977 0.40415 3.18471
8 2OG2 MLI 0.0009072 0.48158 3.52423
9 2HHP FLC 0.003917 0.45982 3.52423
10 2WPB ZZI 0.007678 0.42861 3.52423
11 1M2Z BOG 0.0174 0.42043 3.96476
12 2B6N ALA PRO THR 0.014 0.41226 3.96476
13 2ZTG A5A 0.007621 0.40383 3.96476
14 4RW3 SHV 0.001083 0.48591 4.30464
15 1D8C GLV 0.01504 0.40317 4.84582
16 2JHP GUN 0.01997 0.41559 5.28634
17 5EOO CIT 0.01207 0.42322 5.72687
18 1VPD TLA 0.02772 0.40206 6.60793
19 5G41 AP5 0.002666 0.44597 7.17489
20 4MKF AP5 0.01368 0.40933 7.37327
21 4MKG AP5 0.01393 0.408 8.29493
22 5HTX ADP 0.01362 0.40716 8.37004
23 3BY8 MLT 0.02268 0.40563 8.4507
24 1MLD CIT 0.0259 0.40146 9.2511
25 3I7V ATP 0.003 0.43694 9.70149
26 1W62 PYC 0.01803 0.40957 10.1322
27 1LNX URI 0.002774 0.45548 24.6914
28 2Y69 CHD 0.02966 0.40084 31.4286
Pocket No.: 3; Query (leader) PDB : 1KDO; Ligand: C; Similar sites found: 15
This union binding pocket(no: 3) in the query (biounit: 1kdo.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5O4J SAH 0.01586 0.41064 2.20264
2 5O4J 9KH 0.01586 0.41064 2.20264
3 5O4J PJL 0.01651 0.4087 2.20264
4 1DEK DGP 0.007576 0.40568 2.20264
5 1QO8 FAD 0.01824 0.41547 3.96476
6 3ZEU AGS 0.005838 0.41446 4.40529
7 3ZEU ADP 0.005218 0.41296 4.40529
8 5K2M ADP 0.01353 0.40103 4.84582
9 2Z9I GLY ALA THR VAL 0.0233 0.40467 7.04846
10 2V3V MGD 0.04985 0.41035 8.81057
11 2F5X ASP 0.01862 0.40334 10.5769
12 2J5V PCA 0.004935 0.40116 14.0969
13 2UUU FAD 0.03851 0.40684 14.978
14 2UUU PL3 0.03851 0.40684 14.978
15 3UVD MB3 0.01912 0.40231 35.4839
Pocket No.: 4; Query (leader) PDB : 1KDO; Ligand: C; 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: 1kdo.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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