Receptor
PDB id Resolution Class Description Source Keywords
1DQX 2.4 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP) SACCHAROMYCES CEREVISIAE OROTIDINE 5-prime PHOSPHATE DECARBOXYLASE URIDINE 5-prime PHOSPHATE UMP OMP 6-HYDROXYURIDINE 5-prime -PHOSPHATE BMP TIM BARREL LYASE
Ref.: ANATOMY OF A PROFICIENT ENZYME: THE STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE IN THE PRESENCE AND ABSENCE OF A POTENTIAL TRANSITION STATE ANALOG. PROC.NATL.ACAD.SCI.USA V. 97 2011 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BMP A:601;
B:602;
C:603;
D:604;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 9 pM
340.181 C9 H13 N2 O10 P C1=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DQX 2.4 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP) SACCHAROMYCES CEREVISIAE OROTIDINE 5-prime PHOSPHATE DECARBOXYLASE URIDINE 5-prime PHOSPHATE UMP OMP 6-HYDROXYURIDINE 5-prime -PHOSPHATE BMP TIM BARREL LYASE
Ref.: ANATOMY OF A PROFICIENT ENZYME: THE STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE IN THE PRESENCE AND ABSENCE OF A POTENTIAL TRANSITION STATE ANALOG. PROC.NATL.ACAD.SCI.USA V. 97 2011 2000
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1DQX Ki = 9 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3GDT - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 3GDL - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1DQX Ki = 9 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3GDT - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 3GDL - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3EWZ ic50 = 79 uM CNU C10 H12 N3 O9 P C1=C(C(=O)....
2 3EX2 ic50 ~ 200 uM 6CN C10 H12 N3 O9 P C1=C(N(C(=....
3 2QCG - 5BU C9 H12 Br N2 O9 P C1=C(C(=O)....
4 3MI2 Ki = 0.0000251 mM PFU C9 H14 N3 O9 P C([C@@H]1[....
5 3L0N ic50 = 1680 uM S5P C9 H13 N2 O9 P S C1=C(N(C(=....
6 2QCL - OMP C10 H13 N2 O11 P C1=C(N(C(=....
7 3L0K ic50 = 24 uM 6AU C11 H15 N2 O10 P CC(=O)C1=C....
8 3EWY - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EX1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
10 3EX4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
11 2QCF - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
12 2QCM - JW5 C10 H15 N2 O10 P C1=C(N(C(=....
13 2QCH - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 3EWX - BMP C9 H13 N2 O10 P C1=C(N(C(=....
15 1DQX Ki = 9 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3GDT - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
17 3GDL - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 4HKP - TKW C9 H14 N3 O9 P C1=C(C(=NC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BMP; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 BMP 1 1
2 S5P 0.692308 0.943662
3 U6M 0.681818 0.955882
4 NUP 0.681818 0.971014
5 JW5 0.671642 0.942029
6 6AU 0.642857 0.955882
7 6CN 0.642857 0.928571
8 OMP 0.642857 0.955882
9 O7M 0.608108 0.928571
10 O7E 0.592105 0.928571
11 BMQ 0.573529 0.898551
12 FNU 0.534247 0.917808
13 UP6 0.513889 0.847222
14 U5P 0.513889 0.955224
15 8OP 0.5125 0.815789
16 8GM 0.4875 0.868421
17 H2U 0.479452 0.873239
18 5FU 0.466667 0.915493
19 5BU 0.454545 0.915493
20 2OM 0.448718 0.885714
21 CNU 0.4375 0.928571
22 TKW 0.417722 0.915493
23 H6Y 0.417582 0.828947
24 8OD 0.41573 0.828947
25 CAR 0.405063 0.901408
26 C 0.405063 0.901408
27 C5P 0.405063 0.901408
28 UTP 0.404762 0.970149
29 UDP 0.402439 0.970149
30 44P 0.4 0.928571
31 ICR 0.4 0.821918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DQX; Ligand: BMP; Similar sites found: 99
This union binding pocket(no: 1) in the query (biounit: 1dqx.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3BY8 MLT 0.02008 0.41023 None
2 4YVN EBS 0.01492 0.41662 1.49813
3 3WJO IPE 0.02278 0.40685 1.49813
4 4YMZ 13P 0.004094 0.43924 1.59363
5 3MMH SME 0.009584 0.41634 1.79641
6 1QDS PGA 0.002938 0.44142 1.99203
7 3KDN CAP 0.005512 0.4308 2.24719
8 4IP7 FLC 0.007676 0.43039 2.24719
9 1CKM GTP 0.009574 0.42075 2.24719
10 1PZ1 NAP 0.006827 0.40573 2.24719
11 1SW0 PGA 0.003738 0.43171 2.41935
12 3OPT AKG 0.01175 0.42224 2.62172
13 4QNW FMN 0.004487 0.40545 2.62172
14 4AF0 IMP 0.005156 0.40466 2.62172
15 4H3P ANP 0.008875 0.40265 2.62172
16 1QPR PPC 0.006934 0.40069 2.62172
17 2W5P CL8 0.02689 0.40354 2.68456
18 1Z4O GL1 0.01151 0.40462 2.71493
19 2BTM PGA 0.002672 0.44851 2.77778
20 4I9A NCN 0.002143 0.43011 2.99625
21 3ZGJ RMN 0.01561 0.41449 2.99625
22 1WDD CAP 0.003618 0.40612 2.99625
23 3KRU FMN 0.01013 0.40479 2.99625
24 3AXK NDP 0.01104 0.40186 2.99625
25 2FFC U5P 0.00000009957 0.61441 3.37079
26 3W9Z FMN 0.002366 0.4243 3.37079
27 3VKC FPQ 0.001588 0.42428 3.37079
28 3GLC R5P 0.005746 0.42282 3.37079
29 1KBJ FMN 0.003609 0.41609 3.37079
30 1W8S FBP 0.009926 0.40762 3.42205
31 4JEJ 1GP 0.0001161 0.50341 3.68852
32 4V15 PLP 0.003907 0.43079 3.74532
33 1Z6K OAA 0.02784 0.40027 3.74532
34 4NAE 1GP 0.0001359 0.52612 4
35 1LBF 137 0.0009929 0.40752 4.04858
36 4JWX 1N4 0.01469 0.41586 4.11985
37 2R0D 4IP 0.02225 0.40652 4.11985
38 1U8X G6P 0.02828 0.40573 4.11985
39 2VD9 IN5 0.009104 0.40567 4.11985
40 2R09 4IP 0.02451 0.40434 4.11985
41 1JCM 137 0.0006214 0.42717 4.2471
42 2MSB NAG BMA MAN MAN MAN MAN MAN 0.03487 0.40049 4.34783
43 1TRD PGH 0.006238 0.42111 4.4
44 4KCT PYR 0.009598 0.4207 4.49438
45 1C1X HFA 0.01418 0.40408 4.49438
46 1Z48 FMN 0.003008 0.42755 4.86891
47 1Z44 FMN 0.003953 0.42624 4.86891
48 1Z41 FMN 0.003515 0.42448 4.86891
49 4QYS PLR 0.01541 0.40235 4.86891
50 5A5W GUO 0.0002606 0.48374 5.13834
51 1KKR 2AS 0.01433 0.41712 5.24345
52 2OO0 PLP 0.005939 0.41412 5.24345
53 3WQD PLP 999 0.006726 0.40802 5.38462
54 3EXS 5RP 0.00004978 0.52769 5.42986
55 1UJP CIT 0.000771 0.44983 5.53506
56 1LES GLC FRU 0.01408 0.40917 5.76923
57 2JBH 5GP 0.01743 0.40767 5.77778
58 1VKF CIT 0.005006 0.43677 5.85106
59 3B0P FMN 0.00169 0.43893 5.99251
60 1P0Z FLC 0.02541 0.40631 6.10687
61 3R4S SLB 0.002814 0.46182 6.36704
62 3R4S SIA 0.03599 0.40009 6.36704
63 2V63 CAP 0.002103 0.41918 6.42857
64 2V68 CAP 0.002645 0.41854 6.42857
65 2V67 CAP 0.002717 0.41454 6.42857
66 2VDH CAP 0.002746 0.41435 6.42857
67 1IR2 CAP 0.002777 0.41414 6.42857
68 2V6A CAP 0.00233 0.41343 6.42857
69 1HGX 5GP 0.01043 0.41888 6.55738
70 1C1L GAL BGC 0.01679 0.40808 6.56934
71 4BI7 PGA 0.003868 0.44047 6.61479
72 1UZD CAP 0.002033 0.4198 6.71642
73 4EWN 0VR 0.002895 0.42831 6.71937
74 2CJZ PTR 0.02744 0.40571 6.74157
75 3CTL S6P 0.002036 0.42338 6.92641
76 3VY6 BGC BGC 0.01672 0.40248 7.0922
77 2YPI PGA 0.002576 0.4442 7.28745
78 1UZH CAP 0.003685 0.40902 7.37705
79 3OVR 5SP 0.001182 0.4239 7.45614
80 1Y7P RIP 0.02265 0.40215 8.52018
81 3QH2 3NM 0.0002925 0.50323 8.59729
82 3M6W SAM 0.003919 0.42233 8.61423
83 4UTU LRY 0.000137 0.49406 8.73362
84 4UTW RFW 0.0001805 0.44052 8.73362
85 1LYX PGA 0.0009966 0.40844 8.87097
86 1M5W DXP 0.006728 0.43333 9.0535
87 5EYW PGA 0.003368 0.44348 9.63855
88 2F6U CIT 0.000426 0.49486 9.82906
89 1GVF PGH 0.01519 0.41509 10.1124
90 2TPS TPS 0.001132 0.40821 10.5727
91 1RBL CAP 0.001199 0.43126 11.6105
92 2FLI DX5 0.0003179 0.4534 12.7273
93 2NUO BGC 0.02154 0.40555 13.9344
94 2GUD MAN 0.02471 0.40157 13.9344
95 4RLQ 3SK 0.01695 0.41264 14.9813
96 2Q3R FMN 0.004088 0.40359 14.9813
97 5GJO PLP 0.0006348 0.41683 15.3558
98 1Q6O LG6 0.00001314 0.48688 17.1296
99 2GOU FMN 0.01166 0.40327 22.4719
Pocket No.: 2; Query (leader) PDB : 1DQX; Ligand: BMP; 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: 1dqx.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1DQX; Ligand: BMP; Similar sites found: 44
This union binding pocket(no: 3) in the query (biounit: 1dqx.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4K6B GLU 0.03135 0.40032 None
2 2YN4 39J 0.03426 0.40008 1.27119
3 2DKD NG1 0.0239 0.40232 1.87266
4 1OF8 G3P 0.01134 0.40657 2.24719
5 1OYF MHN 0.02812 0.40159 2.47934
6 2WL9 MBD 0.01733 0.41446 2.62172
7 2GVJ DGB 0.004598 0.41005 2.62172
8 3GAY P6T 0.006553 0.40345 2.62172
9 3KRB NAP 0.008269 0.40194 2.62172
10 1AFS NAP 0.009536 0.40059 2.62172
11 1ZUA TOL 0.01208 0.41697 2.99625
12 1ZUA NAP 0.01208 0.41697 2.99625
13 5UQD AKG 0.01994 0.41092 2.99625
14 3O94 NCA 0.02331 0.40506 3.31754
15 2BGS NDP 0.004643 0.41525 3.37079
16 2WT9 NIO 0.03197 0.40064 3.40426
17 1B09 PC 0.02912 0.40223 3.8835
18 2VD9 EPC 0.01105 0.40007 4.11985
19 1MAI I3P 0.02006 0.40522 4.58015
20 2B4B B33 0.02294 0.40447 4.67836
21 2QLU ADE 0.01024 0.41865 4.86891
22 1Z42 FMN 0.01079 0.41141 4.86891
23 4OB6 S2T 0.01243 0.40115 4.86891
24 1MZV AMP 0.006009 0.42797 5.53191
25 4TO8 FLC 0.006407 0.41638 5.61798
26 4XH0 ADP 0.007651 0.43365 5.99251
27 2OVW CBI 0.01356 0.4148 5.99251
28 2XIQ 5AD 0.01465 0.41753 6.36704
29 4BCQ TJF 0.01644 0.41057 6.36704
30 2WEL K88 0.02338 0.4085 6.66667
31 2FJK 13P 0.01025 0.41658 6.74157
32 4Q4K FMN 0.005771 0.40431 6.74157
33 2PL3 ADP 0.02324 0.40294 6.77966
34 3UKR CKH 0.01541 0.40785 8.60927
35 2INV FRU FRU 0.02649 0.40621 8.61423
36 1N4K I3P 0.02837 0.40179 8.61423
37 3RFA SAM 0.01099 0.40017 9.3633
38 1OX5 1PR 0.001151 0.40199 9.73783
39 3RC3 ANP 0.004282 0.44002 10.4869
40 3SUT OAN 0.01509 0.4083 10.4869
41 2EPN NGT 0.02954 0.40509 10.8614
42 1L5Y BEF 0.001288 0.47268 12.2581
43 2VHL GLP 0.01894 0.40343 14.2322
44 2FKA BEF 0.004921 0.43845 46.6667
Pocket No.: 4; Query (leader) PDB : 1DQX; Ligand: BMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1dqx.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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