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Receptor
PDB id Resolution Class Description Source Keywords
1BO8 2.4 Å EC: 2.1.1.45 THYMIDYLATE SYNTHASE R178T MUTANT LACTOBACILLUS CASEI TRANSFERASE (METHYLTRANSFERASE) TRANSFERASE METHYLTRANSFERNUCLEOTIDE BIOSYNTHESIS
Ref.: ENERGETIC CONTRIBUTIONS OF FOUR ARGININES TO PHOSPHATE-BINDING IN THYMIDYLATE SYNTHASE ARE MORE ADDITIVE AND DEPEND ON OPTIMIZATION OF "EFFECTIVE C BALANCE". BIOCHEMISTRY V. 39 1011 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:317;
Part of Protein;
none;
submit data
39.098 K [K+]
U A:318;
Valid;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
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: U; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 U 1 1
2 U5P 1 1
3 44P 0.790323 0.941176
4 UDP 0.78125 0.984615
5 UTP 0.746269 0.984615
6 2KH 0.735294 0.955224
7 UDP UDP 0.727273 0.953846
8 UPU 0.694444 0.954545
9 UNP 0.690141 0.955224
10 660 0.662338 0.913043
11 URM 0.662338 0.913043
12 URI 0.661017 0.848485
13 GUD 0.641026 0.926471
14 UFM 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GDU 0.641026 0.926471
17 UPF 0.6375 0.875
18 U2F 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 3UC 0.588235 0.875
27 U U 0.585366 0.969697
28 UGB 0.583333 0.940298
29 USQ 0.583333 0.807692
30 UGA 0.583333 0.940298
31 5FU 0.57971 0.927536
32 G3N 0.576471 0.9
33 UA3 0.573529 0.953846
34 U3P 0.573529 0.953846
35 CAR 0.571429 0.941176
36 C 0.571429 0.941176
37 C5P 0.571429 0.941176
38 UDM 0.568182 0.9
39 5BU 0.56338 0.927536
40 U4S 0.557143 0.763889
41 UD1 0.555556 0.913043
42 UD2 0.555556 0.913043
43 CSQ 0.550562 0.863014
44 CSV 0.550562 0.863014
45 U2S 0.541667 0.777778
46 U3S 0.541667 0.763889
47 CNU 0.540541 0.941176
48 S5P 0.535211 0.901408
49 16B 0.534247 0.901408
50 U2P 0.528571 0.939394
51 DU 0.527778 0.911765
52 UMP 0.527778 0.911765
53 HP7 0.526882 0.926471
54 UD7 0.526882 0.913043
55 MJZ 0.521277 0.9
56 UP6 0.521127 0.884058
57 12V 0.515789 0.887324
58 F5G 0.515789 0.913043
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 F5P 0.515789 0.9
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 NUP 0.506849 0.927536
66 U6M 0.506849 0.969697
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 4TC 0.5 0.818182
71 JW5 0.5 0.955224
72 EEB 0.49505 0.887324
73 A U 0.49505 0.815789
74 EPU 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 OMP 0.480519 0.969697
78 6AU 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 G U 0.471154 0.797468
87 5HM 0.467532 0.888889
88 O7E 0.463415 0.941176
89 ICR 0.460526 0.830986
90 UMA 0.458716 0.9
91 O7M 0.45679 0.941176
92 UC5 0.455696 0.885714
93 UTP U U U 0.454545 0.909091
94 CDP 0.45 0.927536
95 2TU 0.449275 0.760563
96 FNU 0.441558 0.876712
97 2QR 0.439655 0.810127
98 DUD 0.4375 0.898551
99 N3E 0.4375 0.743243
100 2OM 0.435897 0.925373
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 U22 0.434783 0.777778
104 DUT 0.433735 0.898551
105 HF4 0.433735 0.927536
106 CTP 0.433735 0.927536
107 8OP 0.428571 0.849315
108 8GM 0.421687 0.853333
109 5GW 0.420455 0.927536
110 U A A U 0.418803 0.853333
111 4RA 0.414634 0.842105
112 DUP 0.411765 0.873239
113 DUN 0.409639 0.873239
114 UD0 0.408 0.831169
115 UVC 0.407895 0.842857
116 UM3 0.407895 0.897059
117 C5G 0.404255 0.875
118 UPA 0.401869 0.828947
119 A U C C 0.401639 0.794872
120 UAG 0.4 0.851351
121 A G U 0.4 0.7875
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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