Receptor
PDB id Resolution Class Description Source Keywords
1KDT 1.95 Å EC: 2.7.4.14 CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH 2',3'-DIDEOXY-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
DOC A:5407;
B:6407;
Valid;
Valid;
none;
none;
submit data
291.198 C9 H14 N3 O6 P C1C[C...
SO4 A:501;
A:502;
B:601;
Invalid;
Invalid;
Invalid;
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: DOC; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 DOC 1 1
2 DCM 0.540541 0.971429
3 DC 0.540541 0.971429
4 DT DC 0.536082 0.868421
5 2DT 0.506849 0.890411
6 C5P 0.493333 0.902778
7 CAR 0.493333 0.902778
8 C 0.493333 0.902778
9 YYY 0.4875 0.957747
10 DCP 0.464286 0.957747
11 LDC 0.450704 0.808219
12 DCZ 0.450704 0.808219
13 CDP 0.439024 0.890411
14 DCP MG 0.436782 0.891892
15 LTT 0.430556 0.780822
16 3TC 0.424658 0.77027
17 CTP 0.423529 0.890411
18 CDP MG 0.416667 0.828947
19 C3P 0.405063 0.888889
20 C2P 0.405063 0.902778
21 7XL 0.404494 0.866667
22 GCQ 0.402299 0.878378
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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