Receptor
PDB id Resolution Class Description Source Keywords
1KDP 2.3 Å EC: 2.7.4.14 CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-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;
B:601;
Invalid;
Invalid;
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 C MONOPHOSPHATE ESCHERICHIA COLI NUCLEOTIDE MONOPHOSPHATE KINASE TRANSFERASE
Ref.: SUGAR SPECIFICITY OF BACTERIAL CMP KINASES AS REVEA CRYSTAL STRUCTURES AND MUTAGENESIS OF ESCHERICHIA C 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 (7)
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....
7 7CKJ - C5P C9 H14 N3 O8 P C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: C; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 C5P 1 1
2 CAR 1 1
3 C 1 1
4 CDP 0.787879 0.985507
5 CTP 0.753623 0.985507
6 HF4 0.753623 0.985507
7 CDP MG 0.735294 0.956522
8 2TM 0.732394 0.944444
9 0RC 0.689189 0.905405
10 7XL 0.689189 0.930556
11 16B 0.676471 0.930556
12 AR3 0.672131 0.842857
13 CTN 0.672131 0.842857
14 C2G 0.662338 0.943662
15 I5A 0.634921 0.828571
16 C5G 0.634146 0.930556
17 CDC 0.62963 0.8375
18 CDM 0.621951 0.881579
19 CXY 0.607143 0.930556
20 TKW 0.591549 0.985507
21 C3P 0.585714 0.956522
22 CDP RB0 0.581395 0.90411
23 5HM 0.575342 0.944444
24 U5P 0.571429 0.941176
25 U 0.571429 0.941176
26 CSQ 0.555556 0.917808
27 CSV 0.555556 0.917808
28 1AA 0.554348 0.893333
29 FZQ 0.548781 0.785714
30 A7R 0.542553 0.917808
31 C2P 0.541667 0.942857
32 PMT 0.540816 0.860759
33 DC 0.540541 0.902778
34 DCM 0.540541 0.902778
35 HQ5 0.523256 0.767442
36 DKZ 0.521127 0.733333
37 YSC 0.5 0.776471
38 G G 6MZ C 0.5 0.825
39 91P 0.495146 0.839506
40 FN5 0.495146 0.858974
41 DOC 0.493333 0.902778
42 5BU 0.486842 0.876712
43 ICR 0.486842 0.861111
44 2AA 0.485714 0.683673
45 MCN 0.485714 0.807229
46 GPC 0.481481 0.829268
47 NCC 0.481132 0.905405
48 G C 0.481132 0.848101
49 5FU 0.48 0.876712
50 CSF 0.476636 0.858974
51 PCD 0.464286 0.770115
52 C5P SIA 0.458716 0.88
53 YYY 0.451219 0.890411
54 UDP 0.45 0.927536
55 CNU 0.45 0.915493
56 44P 0.448718 0.888889
57 DCP 0.447059 0.890411
58 GTF 0.436782 0.890411
59 V12 0.43617 0.7375
60 NUP 0.435897 0.929577
61 GCQ 0.435294 0.890411
62 UTP 0.433735 0.927536
63 2KH 0.428571 0.901408
64 U5F 0.428571 0.927536
65 UP6 0.428571 0.887324
66 NVG 0.427083 0.719512
67 0KX 0.425287 0.866667
68 S5P 0.423077 0.853333
69 GEO 0.418919 0.77027
70 H2U 0.415584 0.861111
71 UDP UDP 0.414634 0.898551
72 FNU 0.4125 0.88
73 JW5 0.4125 0.901408
74 8GM 0.411765 0.906667
75 LDC 0.410959 0.77027
76 DCZ 0.410959 0.77027
77 UPU 0.409091 0.9
78 6MZ C U 0.408 0.825
79 BMP 0.405063 0.901408
80 BMQ 0.402597 0.885714
81 8OP 0.402299 0.853333
82 UNP 0.402299 0.901408
83 DCT 0.402299 0.890411
84 U6M 0.4 0.914286
Similar Ligands (3D)
Ligand no: 1; Ligand: C; Similar ligands found: 85
No: Ligand Similarity coefficient
1 CH 0.9913
2 PSU 0.9811
3 DU 0.9730
4 UMP 0.9709
5 DUS 0.9706
6 TMP 0.9658
7 UMC 0.9608
8 DDN 0.9577
9 PFU 0.9563
10 5CM 0.9536
11 NYM 0.9519
12 UFP 0.9516
13 BRU 0.9504
14 QBT 0.9498
15 AIR 0.9479
16 5IU 0.9455
17 IMP 0.9444
18 AMZ 0.9441
19 IRP 0.9436
20 AMP 0.9418
21 FDM 0.9412
22 FMP 0.9408
23 U4S 0.9401
24 DA 0.9391
25 D5M 0.9388
26 9L3 0.9387
27 C2R 0.9361
28 U3S 0.9340
29 6CN 0.9337
30 8BR 0.9334
31 NIA 0.9314
32 AS 0.9289
33 6MZ 0.9275
34 U1S 0.9257
35 2DT 0.9214
36 D4M 0.9214
37 6AU 0.9205
38 IRN 0.9202
39 5HU 0.9197
40 U2S 0.9174
41 OMP 0.9161
42 NMN 0.9141
43 IMU 0.9139
44 GAR 0.9132
45 G 0.9124
46 5GP 0.9123
47 M2T 0.9120
48 6MA 0.9117
49 NCN 0.9115
50 71V 0.9084
51 N5O 0.9084
52 T3S 0.9072
53 ZAS 0.9067
54 2OM 0.9062
55 NEC 0.8998
56 DG 0.8994
57 DGP 0.8994
58 8OG 0.8941
59 ATM 0.8938
60 MTA 0.8935
61 FAI 0.8922
62 O8M 0.8897
63 6SY 0.8882
64 CMP 0.8878
65 XMP 0.8870
66 AZU 0.8853
67 RP1 0.8824
68 5QT 0.8820
69 JLN 0.8778
70 DRM 0.8775
71 PZB 0.8769
72 URI 0.8767
73 N8M 0.8767
74 TXS 0.8760
75 SP1 0.8745
76 VKE 0.8735
77 TYD 0.8676
78 ML2 0.8674
79 2GE 0.8669
80 UUA 0.8657
81 O7E 0.8631
82 K6B 0.8628
83 PCG 0.8573
84 35G 0.8573
85 URD 0.8554
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KDO; Ligand: C; 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: 1kdo.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KDO; Ligand: C; 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: 1kdo.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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