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Receptor
PDB id Resolution Class Description Source Keywords
1LCA 2.5 Å EC: 2.1.1.45 LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CB3717 LACTOBACILLUS CASEI NUCLEOTIDE SYNTHASE TRANSFERASE (METHYLTRANSFERASE)
Ref.: REFINED STRUCTURES OF SUBSTRATE-BOUND AND PHOSPHATE-BOUND THYMIDYLATE SYNTHASE FROM LACTOBACILLUS CASEI. J.MOL.BIOL. V. 232 1101 1993
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CB3 A:318;
Valid;
none;
submit data
477.469 C24 H23 N5 O6 C#CCN...
UMP A:317;
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
2G86 2.4 Å EC: 2.1.1.45 L. CASEI THYMIDYLATE SYNTHASE Y261F IN COMPLEX WITH SUBSTRAT LACTOBACILLUS CASEI DUMP-BINDING RESIDUE DUMP COMPLEX THYMIDYLATE SYNTHASE MUTTRANSFERASE
Ref.: THE ROLE OF PROTEIN DYNAMICS IN THYMIDYLATE SYNTHAS CATALYSIS: VARIANTS OF CONSERVED 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)-BINDING TYR-261 BIOCHEMISTRY V. 45 7415 2006
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1LCA - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1VZC - UFP C9 H12 F N2 O8 P C1[C@@H]([....
3 1LCB - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1BO7 - U C9 H13 N2 O9 P C1=CN(C(=O....
5 2G8A - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 1JMI Kd = 0.87 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
7 1VZE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
8 1BO8 - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1BPJ - UMP C9 H13 N2 O8 P C1[C@@H]([....
10 1VZA - UMP C9 H13 N2 O8 P C1[C@@H]([....
11 1NJE Kd = 160 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
12 1JMH - UMP C9 H13 N2 O8 P C1[C@@H]([....
13 1TSL Ki = 0.7 uM A15 C24 H14 Cl2 O4 c1cc2cccc3....
14 2G86 Kd = 0.44 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
15 1VZD - UFP C9 H12 F N2 O8 P C1[C@@H]([....
16 1NJD Kd = 2.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1BP6 - UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1TVV - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 1TVU - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1NJC Kd = 2.8 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
21 1LCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 1TSY Kd = 11 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1BP0 Kd = 4 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
24 1NJA Kd = 0.49 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
25 1VZB - UMP C9 H13 N2 O8 P C1[C@@H]([....
26 2G89 - UMP C9 H13 N2 O8 P C1[C@@H]([....
27 1TSX - UMP C9 H13 N2 O8 P C1[C@@H]([....
28 1JMF Kd = 1.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
29 1JMG Kd = 0.85 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
30 1TVW - UMP C9 H13 N2 O8 P C1[C@@H]([....
31 2G8D - UMP C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1LCA - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1VZC - UFP C9 H12 F N2 O8 P C1[C@@H]([....
3 1LCB - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1BO7 - U C9 H13 N2 O9 P C1=CN(C(=O....
5 2G8A - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 1JMI Kd = 0.87 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
7 1VZE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
8 1BO8 - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1BPJ - UMP C9 H13 N2 O8 P C1[C@@H]([....
10 1VZA - UMP C9 H13 N2 O8 P C1[C@@H]([....
11 1NJE Kd = 160 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
12 1JMH - UMP C9 H13 N2 O8 P C1[C@@H]([....
13 1TSL Ki = 0.7 uM A15 C24 H14 Cl2 O4 c1cc2cccc3....
14 2G86 Kd = 0.44 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
15 1VZD - UFP C9 H12 F N2 O8 P C1[C@@H]([....
16 1NJD Kd = 2.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1BP6 - UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1TVV - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 1TVU - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1NJC Kd = 2.8 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
21 1LCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 1TSY Kd = 11 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1BP0 Kd = 4 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
24 1NJA Kd = 0.49 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
25 1VZB - UMP C9 H13 N2 O8 P C1[C@@H]([....
26 2G89 - UMP C9 H13 N2 O8 P C1[C@@H]([....
27 1TSX - UMP C9 H13 N2 O8 P C1[C@@H]([....
28 1JMF Kd = 1.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
29 1JMG Kd = 0.85 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
30 1TVW - UMP C9 H13 N2 O8 P C1[C@@H]([....
31 2G8D - UMP C9 H13 N2 O8 P C1[C@@H]([....
32 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
50% Homology Family (55)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 C1=CN(C(=O....
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 C1=CN(C(=O....
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: 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 : 2G86; Ligand: UMP; Similar sites found with APoc: 81
This union binding pocket(no: 1) in the query (biounit: 2g86.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
1 1SQL GUN None
2 3G1Z AMP 0.949367
3 4WZ6 ATP 1.37931
4 4NTO 1PW 1.44928
5 3PMA SCR 1.5444
6 5A9A UTP 1.64609
7 3B8I OXL 1.74216
8 4URN NOV 1.77778
9 5E70 RCD 2.21519
10 4KVL PLM 2.21519
11 1PFK ADP 2.21519
12 5LX9 OLB 2.28013
13 4TXJ THM 2.36486
14 1YQT ADP 2.53165
15 4OKD GLC GLC GLC 2.53165
16 4KBF AMP 2.53165
17 4P86 5GP 2.73224
18 4JGP PYR 2.76498
19 2D2F ADP 2.8
20 4UYW H1S 2.8481
21 5EQ8 HSO 2.88809
22 3BP1 GUN 3.10345
23 5TDF ADE 3.16456
24 3S6X SIA GAL BGC 3.16456
25 2BVE PH5 3.36134
26 4DE3 DN8 3.42205
27 2BHW NEX 3.44828
28 2Q8M AMP 3.48101
29 1EQ2 ADQ 3.54839
30 3FIU POP 3.61446
31 1PZM 5GP 3.79147
32 2CXG GLC GLC 3.79747
33 3B6C SDN 3.84615
34 5L4R CPT 3.86473
35 2PZE ATP 3.93013
36 6CB2 OLC 4.09556
37 5CQG 55C 4.11392
38 4WBD CIT 4.11392
39 3BHO B4P 4.32692
40 2AK3 AMP 4.42478
41 3B5J 12D 4.52675
42 1DQN IMU 4.78261
43 4URG C2E 4.79042
44 4G86 BNT 4.92958
45 2WOR 2AN 5
46 5NC1 NAG 5.06329
47 4HE2 AMP 5.06329
48 3THR C2F 5.11945
49 5O0X FAD 5.15464
50 5X3R 7Y3 5.36585
51 3MGB GHP 3MY 3FG GHP GHP OMY 3FG 5.37975
52 1J78 OLA 5.37975
53 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 5.78231
54 4M44 SIA GAL NAG GAL 6.04396
55 1EWY FAD 6.12245
56 3DKP ADP 6.12245
57 1W55 GPP 6.32911
58 4CS9 AMP 6.87831
59 1QHO MAL 6.96203
60 2ZWS PLM 7.27848
61 2IW3 ADP 7.27848
62 1QK3 5GP 7.29614
63 1S14 NOV 7.73196
64 3JUC PCA 7.84314
65 2BO4 FLC 7.91139
66 5F1V 3VN 8.08081
67 2YDW WSH 8.49673
68 5CX6 CDP 9.17722
69 6GNO XDI 9.62963
70 5URY PAM 10.274
71 1NJJ GET 10.7595
72 3IWD M2T 11.2903
73 5Y80 IRE 11.4865
74 6C0B PAM 11.5385
75 6C0B MLI 11.5385
76 6FX2 FUC C4W NAG BMA MAN NAG GAL 11.6279
77 3IUY AMP 12.2807
78 5B6D C5P 15.1899
79 3KPE TM3 15.6863
80 4OGQ 7PH 17.2414
81 1B5E DCM 21.5447
Pocket No.: 2; Query (leader) PDB : 2G86; Ligand: UMP; 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: 2g86.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
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