Receptor
PDB id Resolution Class Description Source Keywords
4LRR 2.41 Å EC: 2.1.1.45 TERNARY COMPLEX BETWEEN E. COLI THYMIDYLATE SYNTHASE, DUMP, THYMIDYLATE SYNTHASE ESCHERICHIA COLI
Ref.: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE SUBSTRATE DISPLACE THYMIDYLATE SYNTHASE THROUGH 6-HYDROXY-2H-NAPHTHO[1,8-BC]FURAN-2-ONE DERIVATIVES J.MED.CHEM. V. 56 9356 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:305;
A:304;
A:303;
A:301;
A:308;
A:307;
A:302;
A:306;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
CF9 A:309;
Valid;
none;
Ki = 6 uM
335.267 C18 H9 N O6 c1cc2...
UMP A:310;
Valid;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2KCE 2.2 Å EC: 2.1.1.45 BINDING OF THE ANTICANCER DRUG ZD1694 TO E. COLI THYMIDYLATE ASSESSING SPECIFICITY AND AFFINITY ESCHERICHIA COLI METHYLTRANSFERASE REACTION INTERMEDIATE ANTIFOLATE DRUG D
Ref.: BINDING OF THE ANTICANCER DRUG ZD1694 TO E. COLI TH SYNTHASE: ASSESSING SPECIFICITY AND AFFINITY. STRUCTURE V. 4 1317 1996
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
2 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
5 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
6 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
8 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
9 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
10 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
11 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
12 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
13 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
2 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
5 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
6 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
8 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
9 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
10 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
11 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
12 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
13 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
50% Homology Family (55)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4E28 Ki = 1.3 uM 0MZ C19 H15 F3 N4 O3 S c1ccc(c(c1....
2 1LCA - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 1VZC - UFP C9 H12 F N2 O8 P C1[C@@H]([....
4 1LCB - TMP C10 H15 N2 O8 P CC1=CN(C(=....
5 1BO7 - U C9 H13 N2 O9 P O=C1N(C2OC....
6 2G8A - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 1JMI Kd = 0.87 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
8 1VZE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
9 1BO8 - U C9 H13 N2 O9 P O=C1N(C2OC....
10 1BPJ - UMP C9 H13 N2 O8 P C1[C@@H]([....
11 1VZA - UMP C9 H13 N2 O8 P C1[C@@H]([....
12 1NJE Kd = 160 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
13 1JMH - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1TSL Ki = 0.7 uM A15 C24 H14 Cl2 O4 c1cc2cccc3....
15 2G86 Kd = 0.44 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
16 1VZD - UFP C9 H12 F N2 O8 P C1[C@@H]([....
17 1NJD Kd = 2.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1BP6 - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 1TVV - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1TVU - UMP C9 H13 N2 O8 P C1[C@@H]([....
21 1NJC Kd = 2.8 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
22 1LCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1TSY Kd = 11 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
24 1BP0 Kd = 4 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
25 1NJA Kd = 0.49 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
26 1VZB - UMP C9 H13 N2 O8 P C1[C@@H]([....
27 2G89 - UMP C9 H13 N2 O8 P C1[C@@H]([....
28 1TSX - UMP C9 H13 N2 O8 P C1[C@@H]([....
29 1JMF Kd = 1.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
30 1JMG Kd = 0.85 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
31 1TVW - UMP C9 H13 N2 O8 P C1[C@@H]([....
32 2G8D - UMP C9 H13 N2 O8 P C1[C@@H]([....
33 5X66 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
34 1I00 Kd = 0.46 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
35 1HVY - D16 C21 H22 N4 O6 S CC1=NC(=O)....
36 5X67 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
37 5X5D Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
38 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
39 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
40 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
41 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
42 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
43 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
44 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
45 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
46 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
47 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
48 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
49 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
50 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
51 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
52 5H39 - UMP C9 H13 N2 O8 P C1[C@@H]([....
53 5H3A - D16 C21 H22 N4 O6 S CC1=NC(=O)....
54 1F28 Ki = 16 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
55 2AAZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CF9; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 CF9 1 1
Ligand no: 2; Ligand: UMP; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 UMP 1 1
2 DU 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUT MG 0.684932 0.914286
10 DUR 0.683333 0.852941
11 UMP AF3 PO4 0.675676 0.876712
12 DDN 0.632353 1
13 UFP 0.591549 0.929577
14 BRU 0.583333 0.929577
15 5HU 0.583333 0.942857
16 TMP 0.583333 0.956522
17 UM3 0.57971 0.955224
18 5IU 0.575342 0.929577
19 DCM 0.561644 0.928571
20 DC 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U5P 0.527778 0.911765
24 DDU 0.523077 0.753623
25 UMC 0.520548 0.941176
26 QBT 0.493333 0.927536
27 DUA 0.487805 0.783784
28 DU3 0.487805 0.780822
29 DU4 0.47619 0.76
30 TYD 0.469136 0.942857
31 YYY 0.451219 0.915493
32 UDP 0.45 0.898551
33 TTP 0.447059 0.942857
34 8OG 0.435294 0.835443
35 UA3 0.434211 0.897059
36 U3P 0.434211 0.897059
37 U2P 0.434211 0.884058
38 UTP 0.433735 0.898551
39 44P 0.43038 0.914286
40 DCP 0.430233 0.915493
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 139 0.409091 0.8
45 UPU 0.409091 0.871429
46 U 0.408451 0.771429
47 URI 0.408451 0.771429
48 TBD 0.406977 0.90411
49 PUA 0.405172 0.833333
50 UNP 0.402299 0.873239
51 UDX 0.4 0.873239
52 UAD 0.4 0.873239
53 PUP 0.4 0.955882
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2KCE; Ligand: D16; Similar sites found: 40
This union binding pocket(no: 1) in the query (biounit: 2kce.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PZM 5GP 0.04879 0.40618 0.947867
2 1GT6 OLA 0.04085 0.40343 1.89394
3 2D2F ADP 0.0268 0.42026 2
4 3HAV ATP 0.007273 0.45707 2.27273
5 4GK9 MAN BMA MAN MAN MAN 0.02771 0.42371 2.27273
6 1UJP CIT 0.03048 0.40058 2.27273
7 3TW1 AHN 0.04085 0.41518 2.53165
8 4URG C2E 0.03419 0.41842 2.99401
9 5JDA SIN 0.01133 0.44762 3.0303
10 2UYQ SAM 0.01858 0.43259 3.0303
11 2Q2A ARG 0.03596 0.4063 3.0303
12 3LST SAH 0.03676 0.40257 3.0303
13 3DKP ADP 0.02726 0.41613 3.26531
14 1I0B PEL 0.03009 0.42237 3.40909
15 3OBT SLB 0.01283 0.42846 3.78788
16 1GOJ ADP 0.03666 0.41655 3.78788
17 4C2C ALA ALA ALA 0.03463 0.40953 3.78788
18 5HWK BEZ 0.0448 0.41135 4.16667
19 3B6C SDN 0.03116 0.4208 4.2735
20 1GXU 2HP 0.04934 0.41786 4.3956
21 3FIU POP 0.01302 0.44497 4.41767
22 1QHO MAL 0.008869 0.43814 4.54545
23 1JI0 ATP 0.04378 0.41255 4.58333
24 1T5C ADP 0.02937 0.41988 4.92424
25 4NRT 2NG 0.02916 0.41924 4.92424
26 4KFU ACP 0.03749 0.41889 5.18868
27 3JQ3 ADP 0.04777 0.40318 5.30303
28 3LM9 ADP 0.04227 0.40265 6.06061
29 2BES RES 0.04713 0.40019 6.39535
30 4URN NOV 0.02236 0.42879 7.11111
31 2XT3 ADP 0.04831 0.41187 8.33333
32 4N14 WR7 0.04556 0.40566 9.09091
33 3IUY AMP 0.02819 0.41535 10.9649
34 2D81 RB3 0.03492 0.40697 10.9848
35 3HY2 ATP 0.03202 0.41615 13.6364
36 3CYI ATP 0.03629 0.41876 14.5455
37 4DS0 A2G GAL NAG FUC 0.01899 0.4127 14.7239
38 2VVG ADP 0.04098 0.4147 16.2879
39 4WH9 3M8 0.01865 0.43052 16.3934
40 5B6D C5P 0.000005862 0.58537 28.7879
Pocket No.: 2; Query (leader) PDB : 2KCE; Ligand: D16; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2kce.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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