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Receptor
PDB id Resolution Class Description Source Keywords
1N1D 2 Å EC: 2.7.7.39 GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE COMPLEXED WITH CDP-GLYCEROL BACILLUS SUBTILIS ALPHA/BETA FOLD CYTIDYLYLTRANSFERASE NUCLEOTIDYLTRANSFERASE NEGATIVE COOPERATIVITY CDP-GLYCERO
Ref.: GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE. STRUCTURAL CHANGES INDUCED BY BINDING OF CDP-GLYCEROL AND THE ROLE OF LYSINE RESIDUES IN CATALYSIS J.BIOL.CHEM. V. 278 51863 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2G A:130;
B:230;
C:330;
D:430;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
477.255 C12 H21 N3 O13 P2 C1=CN...
SO4 A:701;
B:705;
D:702;
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
1N1D 2 Å EC: 2.7.7.39 GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE COMPLEXED WITH CDP-GLYCEROL BACILLUS SUBTILIS ALPHA/BETA FOLD CYTIDYLYLTRANSFERASE NUCLEOTIDYLTRANSFERASE NEGATIVE COOPERATIVITY CDP-GLYCERO
Ref.: GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE. STRUCTURAL CHANGES INDUCED BY BINDING OF CDP-GLYCEROL AND THE ROLE OF LYSINE RESIDUES IN CATALYSIS J.BIOL.CHEM. V. 278 51863 2003
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1N1D - C2G C12 H21 N3 O13 P2 C1=CN(C(=O....
2 1COZ - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1N1D - C2G C12 H21 N3 O13 P2 C1=CN(C(=O....
2 1COZ - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1N1D - C2G C12 H21 N3 O13 P2 C1=CN(C(=O....
2 1COZ - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2G; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 C2G 1 1
2 CDM 0.795181 0.933333
3 CDP 0.74026 0.957747
4 CTP 0.734177 0.957747
5 HF4 0.734177 0.957747
6 7XL 0.698795 0.985915
7 C 0.662338 0.943662
8 CAR 0.662338 0.943662
9 C5P 0.662338 0.943662
10 C5G 0.648352 0.958333
11 CDC 0.644444 0.817073
12 CXY 0.623656 0.958333
13 1AA 0.59 0.894737
14 AR3 0.552632 0.871429
15 CTN 0.552632 0.871429
16 C C C C 0.541667 0.930556
17 MCN 0.535714 0.809524
18 2AA 0.535714 0.721649
19 PMT 0.53211 0.8625
20 FN5 0.531532 0.909091
21 91P 0.531532 0.819277
22 C C 0.526316 0.916667
23 I5A 0.525641 0.805556
24 CSF 0.513043 0.909091
25 PCD 0.512605 0.772727
26 C3P 0.494118 0.929577
27 CSQ 0.485714 0.918919
28 CSV 0.485714 0.918919
29 GPC 0.478992 0.809524
30 C2P 0.476744 0.943662
31 16B 0.460674 0.88
32 DKZ 0.458824 0.76
33 C5P SIA 0.458333 0.932432
34 UTP 0.451613 0.901408
35 UDP 0.450549 0.901408
36 DCP 0.447917 0.891892
37 GTF 0.438776 0.866667
38 YYY 0.43617 0.891892
39 UPP 0.435644 0.876712
40 UDH 0.435644 0.881579
41 G C 0.429752 0.82716
42 5HM 0.423913 0.945205
43 UNP 0.42268 0.876712
44 GCQ 0.42268 0.866667
45 UFM 0.417476 0.902778
46 UPG 0.417476 0.902778
47 GDU 0.417476 0.902778
48 GUD 0.417476 0.902778
49 A C A C 0.416 0.848101
50 U A C C 0.416 0.835443
51 U2F 0.40566 0.855263
52 UPF 0.40566 0.855263
53 UFG 0.40566 0.855263
54 660 0.403846 0.916667
55 URM 0.403846 0.916667
56 TKW 0.402174 0.930556
57 UPU 0.4 0.901408
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1N1D; Ligand: C2G; Similar sites found with APoc: 59
This union binding pocket(no: 1) in the query (biounit: 1n1d.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2Y7P SAL None
2 4KJU 1RH None
3 1NXJ TLA None
4 5O2N FLC 2.32558
5 5XET ME8 3.10078
6 5ZDK ATP 3.87597
7 1R6T TYM 3.87597
8 5Y0Q APC 4.65116
9 5Y0N ATP 4.65116
10 2PID YSA 4.65116
11 1Q19 SSC 4.65116
12 1T0S BML 5.42636
13 5Z5I XYP 5.42636
14 3T64 DU3 5.42636
15 2X1L ADN 6.20155
16 4J75 TYM 6.20155
17 3C8Z 5CA 6.20155
18 3AFH GSU 7.75194
19 1YID ATP 7.75194
20 1J09 ATP 7.75194
21 1J09 GLU 7.75194
22 1PFY MSP 8.52713
23 1VBH PEP 8.52713
24 5FPE 3TR 8.52713
25 4MAF ADX 9.30233
26 2H29 DND 10.0775
27 3ZIU LSS 10.0775
28 4NRT 2NG 10.0775
29 1DKU AP2 10.0775
30 5N5U AMP 10.8527
31 3R9C ECL 11.6279
32 5DK4 5BX 12.4031
33 5DK4 ATP 12.4031
34 1UKG MMA 13.1783
35 5Y0T TAT 13.9535
36 1F9A ATP 14.7287
37 3UC5 ATP 15.5039
38 1YUM NCN 16.2791
39 3GUZ PAF 17.0543
40 3COW 52H 17.0543
41 2V0C LEU LMS 17.8295
42 3K9W 4PS 19.3798
43 3K9W ADE 19.3798
44 1KQN NAD 20.155
45 5LLT DND 20.9302
46 1K4M NAD 20.9302
47 2QTR NXX 21.7054
48 6CHP F0Y 23.2558
49 1NUS NMN 23.2558
50 1OD6 PNS 24.031
51 4NAT ADP 25.5814
52 1R6U TYM 25.5814
53 4NAT 2W5 25.5814
54 3ND6 ATP 27.1318
55 5O0B 9FE 27.907
56 1O6B ADP 29.4574
57 5FPN KYD 33.3333
58 1V47 ADX 34.8837
59 2X0K PPV 48.8372
Pocket No.: 2; Query (leader) PDB : 1N1D; Ligand: C2G; Similar sites found with APoc: 24
This union binding pocket(no: 2) in the query (biounit: 1n1d.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1V1A KDG 2.32558
2 5WHU SIA GAL GLC 3.87597
3 5WHU SIA 3.87597
4 5XHA FRU 4.65116
5 2CHT TSA 5.51181
6 1JZS MRC 6.20155
7 2ZUV NDG 6.20155
8 4YRD 3IT 6.97674
9 6FMC DUE 7.59494
10 4FHT DHB 7.75194
11 5A7V MAN 7.75194
12 5A7V BMA 7.75194
13 5LWY OLB 9.30233
14 3KFL ME8 10.0775
15 2X3F APC 10.8527
16 3L24 GOA 12.4031
17 4YP5 NAP 13.9535
18 3NBK PNS 15.5039
19 6EXF LYS 17.8295
20 5Z84 PGV 21.1765
21 2DYR PGV 21.1765
22 5ZCO PGV 21.1765
23 2DYS PGV 21.1765
24 1NUS APC 23.2558
Pocket No.: 3; Query (leader) PDB : 1N1D; Ligand: C2G; Similar sites found with APoc: 30
This union binding pocket(no: 3) in the query (biounit: 1n1d.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3WUD GLC GAL None
2 3VV1 GAL FUC None
3 1TE2 PGA None
4 3OYW TDG None
5 3WV6 GAL BGC 2.32558
6 3E81 SLB 3.10078
7 3RK0 AMP 3.87597
8 4YDX TCE 4.47761
9 1JLX GAL A2G MBN 4.65116
10 1PIG GLC GLC 4.65116
11 3R75 PYR 4.65116
12 5XQL C2E 5.42636
13 3VV5 SLZ 5.42636
14 1A78 TDG 6.20155
15 2VGK REZ 6.20155
16 4IF4 BEF 6.20155
17 5NFB 8VT 6.20155
18 4PB2 5UD 6.20155
19 1HSL HIS 6.97674
20 5CDH TLA 6.97674
21 2CBO TH2 7.82609
22 2XG5 EC5 8.52713
23 2XG5 EC2 8.52713
24 1I7Q PYR 11.6279
25 2YMZ LAT 13.1783
26 3W68 PBU 13.9535
27 1GPM AMP 13.9535
28 1IS3 LAT 15.5039
29 4FRZ ADP 17.0543
30 5DG2 GAL GLC 19.3798
Pocket No.: 4; Query (leader) PDB : 1N1D; Ligand: C2G; Similar sites found with APoc: 14
This union binding pocket(no: 4) in the query (biounit: 1n1d.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3W6X HZP 2.32558
2 1C96 FLC 3.87597
3 2RC8 DSN 3.87597
4 1PCA CIT 5.42636
5 1PFK ADP 5.42636
6 1OIJ AKG 6.20155
7 2B7N NTM 6.97674
8 2WL9 MBD 6.97674
9 4B2D SER 7.75194
10 5K6A 6QT 8.52713
11 5LQ8 GB 10.0775
12 1JQY A32 10.6796
13 2RCA GLY 10.8527
14 1K4M CIT 20.9302
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