Receptor
PDB id Resolution Class Description Source Keywords
4HKP 1.75 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARB COMPLEXED WITH CMP-N3-OXIDE HOMO SAPIENS ALPHA-BETA BARREL DECARBOXYLASE LYASE-LYASE INHIBITOR COMP
Ref.: NOVEL CYTIDINE-BASED OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE INHIBITORS WITH AN UNUSUAL TWIST. J.MED.CHEM. V. 55 9988 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
16B A:305;
Valid;
none;
submit data
339.196 C9 H14 N3 O9 P C1=CN...
GOL A:301;
A:302;
A:303;
B:301;
B:302;
B:303;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TKW A:304;
B:304;
Valid;
Valid;
none;
none;
submit data
339.196 C9 H14 N3 O9 P C1=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4HKP 1.75 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARB COMPLEXED WITH CMP-N3-OXIDE HOMO SAPIENS ALPHA-BETA BARREL DECARBOXYLASE LYASE-LYASE INHIBITOR COMP
Ref.: NOVEL CYTIDINE-BASED OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE INHIBITORS WITH AN UNUSUAL TWIST. J.MED.CHEM. V. 55 9988 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4HKP - TKW C9 H14 N3 O9 P C1=C(C(=NC....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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 4HKP - TKW C9 H14 N3 O9 P C1=C(C(=NC....
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: 16B; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 16B 1 1
2 C 0.676471 0.930556
3 CAR 0.676471 0.930556
4 C5P 0.676471 0.930556
5 CDP 0.538462 0.917808
6 U5P 0.534247 0.901408
7 TKW 0.533333 0.917808
8 5HM 0.519481 0.881579
9 CTP 0.518519 0.917808
10 CDP MG 0.493827 0.855263
11 7XL 0.476744 0.868421
12 ICR 0.474359 0.851351
13 5FU 0.467532 0.842105
14 C2G 0.460674 0.88
15 5BU 0.455696 0.842105
16 C C 0.455556 0.878378
17 C5G 0.446809 0.868421
18 CTN 0.444444 0.783784
19 AR3 0.444444 0.783784
20 CDC 0.44086 0.785714
21 CNU 0.439024 0.878378
22 CDM 0.43617 0.825
23 CXY 0.427083 0.868421
24 CH 0.425 0.916667
25 H2U 0.423077 0.826667
26 UDP 0.421687 0.888889
27 44P 0.419753 0.853333
28 2KH 0.418605 0.890411
29 UP6 0.417722 0.876712
30 S5P 0.4125 0.820513
31 U6M 0.407407 0.876712
32 UTP 0.406977 0.888889
33 PMT 0.40367 0.807229
34 JW5 0.402439 0.864865
35 I5A 0.4 0.77027
Ligand no: 2; Ligand: TKW; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 TKW 1 1
2 5HM 0.681159 0.958333
3 CAR 0.591549 0.985507
4 C 0.591549 0.985507
5 C5P 0.591549 0.985507
6 16B 0.533333 0.917808
7 5FU 0.513514 0.890411
8 CDP 0.4875 0.971429
9 5BU 0.480519 0.890411
10 U5P 0.48 0.927536
11 CTP 0.46988 0.971429
12 CNU 0.4625 0.929577
13 ICR 0.461538 0.849315
14 F01 0.458333 0.8
15 UP6 0.441558 0.875
16 NUP 0.43038 0.943662
17 CDP MG 0.428571 0.90411
18 BMP 0.417722 0.915493
19 S5P 0.417722 0.866667
20 7XL 0.41573 0.917808
21 H2U 0.410256 0.849315
22 JW5 0.407407 0.915493
23 FNU 0.407407 0.893333
24 8GM 0.406977 0.92
25 C2G 0.402174 0.930556
26 CDC 0.4 0.82716
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4HKP; Ligand: TKW; Similar sites found: 92
This union binding pocket(no: 1) in the query (biounit: 4hkp.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QB7 ADE 0.01433 0.40941 1.27119
2 2BTM PGA 0.003019 0.44765 1.5873
3 1LBF 137 0.001892 0.40025 2.02429
4 4UTU LRY 0.0002087 0.48766 2.18341
5 4UTW RFW 0.0002402 0.47945 2.18341
6 1ME8 RVP 0.007944 0.41102 2.5641
7 4RLQ 3SK 0.03073 0.40078 2.5641
8 5XG5 A2G 0.001664 0.47218 2.75862
9 3VKC FPQ 0.002007 0.42187 2.7972
10 2WW4 ADP 0.01724 0.40163 2.82686
11 3R4S SLB 0.002954 0.46247 2.88462
12 3WQD PLP 999 0.007468 0.4077 2.88462
13 4Q4K FMN 0.006679 0.40165 2.88462
14 2B4B B33 0.01332 0.42132 2.92398
15 3GLC R5P 0.003996 0.4321 3.05085
16 2DUR MAN MAN 0.01403 0.40837 3.16206
17 1KBJ FMN 0.002686 0.41821 3.20513
18 4QNW FMN 0.004158 0.40859 3.20513
19 1PZ1 NAP 0.006402 0.40389 3.20513
20 2F6U CIT 0.0003282 0.5027 3.4188
21 3OVR 5SP 0.001845 0.41992 3.50877
22 4V15 PLP 0.002979 0.4382 3.52564
23 3ZGJ RMN 0.01959 0.41099 3.52564
24 1UZH CAP 0.00339 0.4059 3.52564
25 3B0P FMN 0.001022 0.45077 3.71429
26 1JCM 137 0.001196 0.4107 3.861
27 4JLS 3ZE 0.02121 0.41149 3.94737
28 1QDS PGA 0.002464 0.44696 3.98406
29 2Y88 2ER 0.00341 0.42593 4.09836
30 3P7G MAN 0.02936 0.40283 4.10959
31 4KCT PYR 0.00489 0.43712 4.16667
32 1Z44 FMN 0.003709 0.4293 4.16667
33 1Z41 FMN 0.005128 0.41876 4.16667
34 3KRU FMN 0.005849 0.4122 4.16667
35 1Z42 FMN 0.0151 0.4044 4.16667
36 1IR2 CAP 0.002831 0.4156 4.28571
37 2V67 CAP 0.002841 0.41554 4.28571
38 2V68 CAP 0.003426 0.41553 4.28571
39 2VDH CAP 0.002081 0.41418 4.28571
40 2V63 CAP 0.002097 0.41402 4.28571
41 2V6A CAP 0.002804 0.40525 4.28571
42 4YMZ 13P 0.004492 0.43898 4.38247
43 1LYX PGA 0.0007501 0.40618 4.43548
44 4NAE 1GP 0.0002143 0.51682 4.44444
45 1G1T SIA GAL MAG FUC 0.01637 0.41373 4.4586
46 1RBL CAP 0.001354 0.42544 4.48718
47 3EXS 5RP 0.00004514 0.532 4.80769
48 3KDN CAP 0.007196 0.42248 4.80769
49 3W9Z FMN 0.001103 0.41421 4.80769
50 1KBI PYR 0.002756 0.41929 5.12821
51 4EWN 0VR 0.00408 0.4233 5.13834
52 1GZW GAL BGC 0.03506 0.40103 5.22388
53 2YPI PGA 0.0022 0.44937 5.26316
54 1M5W DXP 0.009692 0.42684 5.34979
55 5F90 GLA GAL 0.0004722 0.50839 5.44872
56 5F90 LMR 0.000837 0.49249 5.44872
57 4YVN EBS 0.02981 0.40235 5.44872
58 5A5W GUO 0.0005262 0.46612 5.5336
59 2NUO BGC 0.01585 0.41703 5.7377
60 2NU5 NAG 0.01562 0.41531 5.7377
61 2HYR BGC GLC 0.01863 0.41335 5.7377
62 2GUC MAN 0.01825 0.40886 5.7377
63 5CSS G3P 0.008066 0.42618 5.75221
64 4A3U FMN 0.003713 0.4036 5.76923
65 2VD9 IN5 0.005957 0.41578 6.08974
66 1CKM GTP 0.01581 0.41142 6.08974
67 2VD9 EPC 0.007716 0.40706 6.08974
68 4RL4 PPV 0.01645 0.40614 6.13208
69 3M6W SAM 0.007907 0.41015 6.41026
70 5EYW PGA 0.002294 0.45365 6.4257
71 3CTL S6P 0.001583 0.41541 6.49351
72 2JBH 5GP 0.01645 0.41055 6.66667
73 1UZD CAP 0.002567 0.41057 6.71642
74 2FLI DX5 0.0004835 0.43917 6.81818
75 1SW0 PGA 0.00304 0.43778 6.85484
76 1Q6O LG6 0.000007407 0.48606 6.94444
77 4RW3 IPD 0.02048 0.40573 6.95364
78 3C2O NTM 0.007227 0.40167 7.48299
79 1JQY A32 0.01997 0.40628 7.76699
80 5TQZ GLC 0.03487 0.40339 8
81 4JEJ 1GP 0.0001995 0.42086 8.19672
82 5TCI MLI 0.007074 0.43481 8.33333
83 3QH2 3NM 0.0001602 0.51875 9.04977
84 1UJP CIT 0.001012 0.44649 9.5941
85 2TPS TPS 0.001694 0.42658 10.1322
86 5HX1 UMP 0.02536 0.40677 10.8696
87 5GJO PLP 0.0006895 0.40939 11.2179
88 5HZX 2GE 0.01101 0.41505 11.9318
89 4I9A NCN 0.004894 0.41591 13.1944
90 1LES GLC FRU 0.01262 0.40896 15.3846
91 2FFC U5P 0.0000001279 0.56397 23.7179
92 1WDD CAP 0.003541 0.40194 25.7812
Pocket No.: 2; Query (leader) PDB : 4HKP; Ligand: 16B; Similar sites found: 90
This union binding pocket(no: 2) in the query (biounit: 4hkp.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BTM PGA 0.003098 0.44146 1.5873
2 1ICP FMN 0.008983 0.40956 1.60256
3 2Q3R FMN 0.002419 0.42199 1.92308
4 2RDT 2RD 0.009164 0.41171 1.92308
5 2RDT FMN 0.006482 0.41171 1.92308
6 2GVJ DGB 0.002936 0.40996 1.92308
7 2HW1 FRU 0.02554 0.40105 2.01342
8 4UTU LRY 0.0002708 0.47593 2.18341
9 4UTW RFW 0.0003567 0.46527 2.18341
10 1ME8 RVP 0.004955 0.42981 2.5641
11 3OPT AKG 0.01188 0.41889 2.5641
12 4RLQ 3SK 0.02469 0.40082 2.5641
13 1QPR PPC 0.005643 0.40788 2.8169
14 4Q4K FMN 0.00311 0.4259 2.88462
15 3CV6 NAP 0.02077 0.40288 2.88462
16 3WQD PLP 999 0.008076 0.40086 2.88462
17 2B4B B33 0.01015 0.42502 2.92398
18 3GLC R5P 0.003283 0.43057 3.05085
19 1KBJ FMN 0.002379 0.43106 3.20513
20 4QNW FMN 0.001839 0.41345 3.20513
21 2BLE 5GP 0.008647 0.40897 3.20513
22 2F6U CIT 0.0003984 0.49205 3.4188
23 3NZ1 3NY 0.02662 0.40224 3.44828
24 3OVR 5SP 0.001113 0.44044 3.50877
25 4XH0 ADP 0.001402 0.46735 3.52564
26 4V15 PLP 0.002244 0.43835 3.52564
27 1UZH CAP 0.002274 0.42506 3.52564
28 4Y9T PA1 0.01334 0.41577 3.52564
29 3ZGJ RMN 0.01522 0.41158 3.52564
30 3B0P FMN 0.001255 0.44075 3.71429
31 4XP7 FNR 0.005432 0.40489 3.84615
32 1JCM 137 0.0008872 0.43398 3.861
33 2Z6J FMN 0.01045 0.40659 3.91566
34 1QDS PGA 0.00307 0.43665 3.98406
35 2Y88 2ER 0.001815 0.44879 4.09836
36 1Z44 FMN 0.002545 0.43125 4.16667
37 4KCT PYR 0.006129 0.42679 4.16667
38 3KRU FMN 0.004662 0.42633 4.16667
39 1Z41 FMN 0.002802 0.4251 4.16667
40 1Z48 FMN 0.001794 0.41634 4.16667
41 1Z42 FMN 0.01041 0.40694 4.16667
42 2VDH CAP 0.001352 0.43487 4.28571
43 2V63 CAP 0.001676 0.43082 4.28571
44 2V6A CAP 0.001688 0.42874 4.28571
45 2V68 CAP 0.002182 0.41617 4.28571
46 2V67 CAP 0.002206 0.41065 4.28571
47 1IR2 CAP 0.002193 0.41042 4.28571
48 4YMZ 13P 0.004902 0.43159 4.38247
49 1LYX PGA 0.002065 0.4076 4.43548
50 4NAE 1GP 0.0001634 0.51696 4.44444
51 1RBL CAP 0.0008872 0.44475 4.48718
52 4RJK PYR 0.01897 0.40615 4.48718
53 3EXS 5RP 0.00003646 0.52943 4.80769
54 3KDN CAP 0.004276 0.44266 4.80769
55 3W9Z FMN 0.0008713 0.43904 4.80769
56 1KBI PYR 0.002394 0.4325 5.12821
57 4EWN 0VR 0.004406 0.41627 5.13834
58 2YPI PGA 0.002005 0.44558 5.26316
59 1M5W DXP 0.01347 0.4143 5.34979
60 5A5W GUO 0.0003618 0.48604 5.5336
61 3UWV 2PG 0.007659 0.4021 5.74713
62 5CSS G3P 0.008082 0.42083 5.75221
63 4A3U FMN 0.003312 0.41795 5.76923
64 2VD9 IN5 0.005446 0.41213 6.08974
65 1TB3 FMN 0.01004 0.40867 6.08974
66 1CKM GTP 0.0145 0.40821 6.08974
67 1OFD FMN 0.01774 0.40308 6.08974
68 2VD9 EPC 0.00794 0.40119 6.08974
69 5EYW PGA 0.002279 0.44806 6.4257
70 3CTL S6P 0.0056 0.40622 6.49351
71 1UZD CAP 0.001517 0.4327 6.71642
72 2FLI DX5 0.0009246 0.44205 6.81818
73 1SW0 PGA 0.002728 0.43436 6.85484
74 1Q6O LG6 0.000008039 0.51198 6.94444
75 3FQ8 PMP 0.007592 0.40559 7.37179
76 1VYP TNF 0.003933 0.4198 7.69231
77 1VYP FMN 0.004266 0.4198 7.69231
78 4JEJ 1GP 0.0003746 0.43063 8.19672
79 5TCI MLI 0.007097 0.43273 8.33333
80 5EFQ ADP 0.00778 0.40158 8.97436
81 3JQA DX4 0.03969 0.40762 9.02778
82 3QH2 3NM 0.0006839 0.48014 9.04977
83 1UJP CIT 0.002852 0.42074 9.5941
84 3FIU POP 0.01531 0.41129 9.63855
85 2TPS TPS 0.004891 0.41716 10.1322
86 5GJO PLP 0.001879 0.41229 11.2179
87 3ATY FMN 0.007033 0.40862 12.5
88 4I9A NCN 0.005268 0.40903 13.1944
89 2FFC U5P 0.0000001291 0.60338 23.7179
90 1WDD CAP 0.002458 0.42169 25.7812
Pocket No.: 3; Query (leader) PDB : 4HKP; Ligand: TKW; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4hkp.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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