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Receptor
PDB id Resolution Class Description Source Keywords
1NCE 2.4 Å EC: 2.1.1.45 CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI THYMIDYLAT D169C WITH DUMP AND THE ANTIFOLATE CB3717 ESCHERICHIA COLI, ESCHERICHIA COLI O15ORGANISM_COMMON:
Ref.: THE ONLY ACTIVE MUTANT OF THYMIDYLATE SYNTHASE D169 RESIDUE FAR FROM THE SITE OF METHYL TRANSFER, DEMON THE EXQUISITE NATURE OF ENZYME SPECIFICITY. PROTEIN ENG. V. 16 229 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CB3 A:566;
B:568;
Valid;
Valid;
none;
none;
submit data
477.469 C24 H23 N5 O6 C#CCN...
UMP A:565;
B:567;
Valid;
Valid;
none;
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
1NCE 2.4 Å EC: 2.1.1.45 CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI THYMIDYLAT D169C WITH DUMP AND THE ANTIFOLATE CB3717 ESCHERICHIA COLI, ESCHERICHIA COLI O15ORGANISM_COMMON:
Ref.: THE ONLY ACTIVE MUTANT OF THYMIDYLATE SYNTHASE D169 RESIDUE FAR FROM THE SITE OF METHYL TRANSFER, DEMON THE EXQUISITE NATURE OF ENZYME SPECIFICITY. PROTEIN ENG. V. 16 229 2003
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1NCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1NCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1JTU - LYB C35 H42 N8 O15 c1cc(ccc1C....
2 1J3K Ki = 0.037 nM WRA C14 H18 Cl3 N5 O2 CC1(N=C(N=....
3 1J3J Ki = 9.8 nM CP6 C12 H13 Cl N4 CCc1c(c(nc....
4 1J3I Ki = 0.011 nM WRA C14 H18 Cl3 N5 O2 CC1(N=C(N=....
5 1NCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 1JTQ - LY3 C20 H21 N9 O4 c1cc(ccc1C....
7 1FWM - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
8 1JG0 ic50 = 5 uM DDT C33 H33 N3 O7 S2 CN(C)c1ccc....
9 1DNA - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
10 1F4F Ki = 24 uM TP3 C17 H20 N2 O9 S c1cc(ccc1C....
11 1SYN Kd = 0.1 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
12 1KCE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
13 1DDU - DDU C9 H12 N2 O4 C[C@@H]1[C....
14 4GEV - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
15 1TLC Kd = 0.076 uM DGP C10 H14 N5 O7 P c1nc2c(n1[....
16 1AIQ - UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1TDU - DUR C9 H12 N2 O5 C1[C@@H]([....
18 1AXW - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 6CDZ - UMC C9 H15 N2 O8 P C1CN(C(=O)....
20 1BQ1 - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
21 1KZI - THG C19 H23 N7 O6 c1cc(ccc1C....
22 1ZPR - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1F4G Ki = 330 nM TP4 C20 H25 N3 O10 S c1cc(ccc1C....
24 1TSD Kd = 0.04 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CB3; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 CB3 1 1
2 PFG 0.902174 0.96875
3 DZF 0.459459 0.861538
4 NHS 0.445455 0.870968
5 3YA 0.433628 0.771429
6 3Y9 0.428571 0.782609
7 D16 0.422414 0.753425
8 9L9 0.419048 0.742857
9 83A 0.417391 0.811594
10 THF 0.40678 0.783784
11 1JY 0.406015 0.811594
12 DDF 0.405172 0.739726
13 21V 0.405172 0.739726
14 DHF 0.403509 0.785714
15 LYA 0.401786 0.794118
16 1YA 0.4 0.828571
Ligand no: 2; Ligand: UMP; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 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 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NCE; Ligand: UMP; Similar sites found with APoc: 24
This union binding pocket(no: 1) in the query (biounit: 1nce.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2FXD DR7 3.0303
2 4P86 5GP 3.27869
3 2CXG GLC GLC 3.78788
4 1KZN CBN 3.90244
5 4Z7X 3CX 4.20168
6 1QHO MAL 4.54545
7 2D24 XYS XYS 4.54545
8 3GFB NAD 4.54545
9 3G6K POP 4.92424
10 3G6K FAD 4.92424
11 4WQQ MAN 4.96454
12 5WHT SIA GAL 5.07246
13 4KQW NAP 5.14286
14 2VBU CDP 5.14706
15 2DFV NAD 6.06061
16 2ZQO NGA 6.92308
17 4OWK NGA 7.97101
18 4P83 U5P 8.24176
19 1GAR U89 9.90566
20 1KNM LAT 10.7692
21 1CSI OAA 10.9848
22 1CSI CMX 10.9848
23 5B6D C5P 28.4091
24 1B5E DCM 31.7073
Pocket No.: 2; Query (leader) PDB : 1NCE; Ligand: CB3; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 1nce.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1GQG DCD 1.89394
2 3WH1 NAG NAG NAG NAG 2.91262
3 1UKZ ADP 2.95567
4 1WVC CTP 3.0888
5 4YMH SAH 3.33333
6 4W6Z 8ID 3.78788
7 4RJK TPP 4.16667
8 5EXE 5SR 5.30303
9 3EXH TPP 6.02094
10 2OZL TPP 6.30137
11 2FR1 NDP 7.57576
12 5SVV FMN 13.1387
13 2D4V NAD 14.0152
Pocket No.: 3; Query (leader) PDB : 1NCE; Ligand: CB3; Similar sites found with APoc: 11
This union binding pocket(no: 3) in the query (biounit: 1nce.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2V54 TYD 2.45098
2 3GE7 AFQ 3.0303
3 3QWB NDP 3.40909
4 2E40 LGC 3.40909
5 2E7Z MGD 3.40909
6 3JYN NDP 3.78788
7 1N9G NAP 3.78788
8 4RJK TDL 4.16667
9 4ZY1 4U5 7.19697
10 5JIB OIA 10.6061
11 2J8Z NAP 19.3182
Pocket No.: 4; Query (leader) PDB : 1NCE; Ligand: UMP; Similar sites found with APoc: 24
This union binding pocket(no: 4) in the query (biounit: 1nce.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1PZM 5GP 1.4218
2 3DLG GWE 1.89394
3 2VL8 CTS 1.89394
4 2VL8 UDP 1.89394
5 5UQK U2F 2.27273
6 1YQS BSA 2.27273
7 4I3V NAD 2.27273
8 2FXV 5GP 2.57732
9 5O3N 4LU 2.65152
10 6FLZ MMA 2.77778
11 2HMT NAI 2.77778
12 5WGR PM7 3.0303
13 1L1Q 9DA 3.22581
14 6APV 3L4 3.24074
15 1E5F PLP 4.16667
16 4BUY F37 4.58333
17 4OUJ LBT 5.30303
18 3R4S SLB 5.68182
19 4JLS 3ZE 5.92105
20 4ZL4 4PK 7.19697
21 3HNB 768 7.54717
22 4XQC NAD 9.09091
23 1RC0 KT5 10.5263
24 6GNO XDI 11.1111
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