Receptor
PDB id Resolution Class Description Source Keywords
1DBT 2.4 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP BACILLUS SUBTILIS DECARBOXYLASE UMP TIM BARREL LYASE
Ref.: THE CRYSTAL STRUCTURE AND MECHANISM OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE. PROC.NATL.ACAD.SCI.USA V. 97 2005 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U5P A:250;
B:251;
C:252;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 0.46 mM
324.181 C9 H13 N2 O9 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DBT 2.4 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP BACILLUS SUBTILIS DECARBOXYLASE UMP TIM BARREL LYASE
Ref.: THE CRYSTAL STRUCTURE AND MECHANISM OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE. PROC.NATL.ACAD.SCI.USA V. 97 2005 2000
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1DBT Ki = 0.46 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1DBT Ki = 0.46 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1DBT Ki = 0.46 mM U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 1EIX Ki = 8.8 pM BMQ C9 H13 N2 O10 P C1C(=O)NC(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U5P; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 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 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 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 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DBT; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1dbt.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1DBT; Ligand: U5P; Similar sites found: 63
This union binding pocket(no: 2) in the query (biounit: 1dbt.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OO0 PLP 0.001792 0.41698 2.51046
2 2Y88 2ER 0.001048 0.45977 2.92887
3 1LBF 137 0.004348 0.42093 2.92887
4 1NJJ ORX 0.003399 0.41746 2.92887
5 5W4W 9WG 0.01342 0.40294 2.92887
6 4TWP AXI 0.01965 0.42079 3.34728
7 1LYX PGA 0.002515 0.40485 3.34728
8 5L4L 7OX 0.01936 0.40334 3.34728
9 5HCY 60D 0.02563 0.40132 3.34728
10 4NAE 1GP 0.0008065 0.48323 3.55556
11 2YPI PGA 0.001532 0.45121 3.76569
12 4JEJ 1GP 0.0001504 0.44603 3.76569
13 2BCG GER 0.01078 0.41462 3.76569
14 1TUF AZ1 0.005234 0.41431 3.76569
15 2VHL GLP 0.01429 0.40436 4.1841
16 1AFS NAP 0.0136 0.40268 4.1841
17 4Z3X MTE 0.04487 0.40113 4.1841
18 3CTL S6P 0.002009 0.42548 4.329
19 4EWN 0VR 0.00429 0.40009 4.34783
20 2NVA PL2 0.004846 0.41734 4.60251
21 1O68 KIV 0.01595 0.41054 4.60251
22 2C6Q NDP 0.02553 0.40226 5.02092
23 1Q6O LG6 0.00001355 0.50344 5.09259
24 3EXS 5RP 0.00003113 0.53274 5.42986
25 2PLK P3D 0.001753 0.42997 5.43933
26 3KRU FMN 0.007193 0.41774 5.43933
27 3C2O NTM 0.01072 0.4034 5.43933
28 4U0I 0LI 0.01024 0.40829 5.85774
29 3VKC FPQ 0.006411 0.40546 5.85774
30 2HSA FMN 0.01349 0.40158 5.85774
31 1SZO CAX 0.02517 0.40076 5.85774
32 1PVN MZP 0.01169 0.41556 6.27615
33 1ME8 RVP 0.01091 0.41392 6.27615
34 1W8S FBP 0.001707 0.41214 6.27615
35 1GVE NAP 0.01573 0.40332 6.27615
36 1M5W DXP 0.0003613 0.47973 6.69456
37 4Q4K FMN 0.003117 0.42585 6.69456
38 2BP1 NDP 0.01179 0.41021 6.69456
39 2C91 NAP 0.0134 0.40764 6.69456
40 3EAU PDN 0.01357 0.40952 7.11297
41 1RBL CAP 0.004447 0.41414 7.33945
42 1LQA NDP 0.01243 0.40914 7.53138
43 3KDN CAP 0.006786 0.4331 7.94979
44 4UTW RFW 0.0002549 0.45046 8.73362
45 4UTU LRY 0.0002013 0.44913 8.73362
46 5A5W GUO 0.000379 0.4851 9.20502
47 5T79 NDP 0.007644 0.41138 9.20502
48 2F6U CIT 0.001253 0.46678 9.82906
49 4I9B 1KA 0.006406 0.40137 10.4603
50 2XMY CDK 0.03921 0.40526 10.8787
51 3B0P FMN 0.0008996 0.42657 11.2971
52 1PZ1 NAP 0.00813 0.41017 11.7155
53 1UJP CIT 0.001974 0.42776 12.5523
54 3OVR 5SP 0.0005361 0.45431 12.7193
55 4P5Z Q7M 0.01279 0.41071 14.6444
56 5GJO PLP 0.0001432 0.45335 15.4812
57 2Z6J FMN 0.004129 0.42479 16.318
58 3W9Z FMN 0.004402 0.40882 16.318
59 1SW0 PGA 0.002248 0.40292 16.318
60 2TPS TPS 0.0009801 0.44816 17.6211
61 2FLI DX5 0.0003867 0.45849 23.6364
62 1Z44 FMN 0.01126 0.40152 28.8703
63 2FFC U5P 0.000001442 0.5584 33.8912
Pocket No.: 3; Query (leader) PDB : 1DBT; Ligand: U5P; Similar sites found: 190
This union binding pocket(no: 3) in the query (biounit: 1dbt.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1C1L GAL BGC 0.0002869 0.48855 None
2 3KPE TM3 0.007269 0.41778 None
3 2FR6 URI 0.0005543 0.41591 None
4 4F4S EFO 0.007871 0.40551 None
5 3WSJ MK1 0.01444 0.40003 None
6 3MPI GRA 0.04187 0.40327 0.83682
7 2EWM NAD 0.003229 0.40796 1.25523
8 2V6O FAD 0.02661 0.40363 1.25523
9 4QN6 LNV 0.002543 0.41902 1.67364
10 2NX1 PEP 0.002366 0.4086 1.67364
11 2NX1 RP5 0.002553 0.40744 1.67364
12 2Q2V NAD 0.0001314 0.46097 2.09205
13 1PEA ACM 0.02155 0.40787 2.09205
14 1DAK ADP 0.002645 0.42162 2.23214
15 1DAK DPU 0.002645 0.42162 2.23214
16 2F01 BTQ 0.02373 0.40176 2.3622
17 2F01 BTN 0.02373 0.40176 2.3622
18 2AQJ TRP 0.005402 0.42344 2.51046
19 2AQJ FAD 0.00563 0.42344 2.51046
20 2BII MTV 0.0006061 0.42267 2.51046
21 3TN7 NJP 0.001332 0.42179 2.51046
22 1TOI HCI 0.001885 0.41357 2.51046
23 4E28 9MZ 0.01036 0.41092 2.51046
24 1VDC FAD 0.007647 0.41065 2.51046
25 3S7O LBV 0.00291 0.40959 2.51046
26 3L02 SN0 0.003648 0.40734 2.51046
27 3L02 CP 0.003648 0.40734 2.51046
28 4CMF PXG 0.01259 0.4039 2.51046
29 1J5P NAD 0.00334 0.40331 2.51046
30 1EB9 HBA 0.0004232 0.40061 2.51046
31 1V2X SAM 0.001044 0.40878 2.57732
32 3R35 4CO 0.003122 0.40849 2.64901
33 1O9U ADZ 0.0005327 0.49471 2.92887
34 4NM5 ADP 0.0003544 0.42877 2.92887
35 4DEM YS4 0.008263 0.42759 2.92887
36 3MAG 3MA 0.01976 0.4235 2.92887
37 1Y42 TYR 0.002916 0.42338 2.92887
38 1TFZ 869 0.0003929 0.42312 2.92887
39 4Q0P 0MK 0.0142 0.42266 2.92887
40 1NVV GNP 0.0008612 0.4209 2.92887
41 3E8N VRA 0.009446 0.40279 2.92887
42 3E8N ATP 0.009446 0.40279 2.92887
43 1H6C SIN 0.008045 0.40255 2.92887
44 1Q11 TYE 0.00006959 0.40236 2.92887
45 1YOA FMN 0.03733 0.41643 3.14465
46 4D7M TDC 0.003265 0.40218 3.22581
47 1EDO NAP 0.007103 0.42463 3.34728
48 1H2B NAJ 0.002744 0.41308 3.34728
49 2NCD ADP 0.006925 0.41306 3.34728
50 1RYI FAD 0.007579 0.40547 3.34728
51 3U4C NDP 0.00352 0.40392 3.34728
52 1I2B USQ 0.01728 0.40148 3.34728
53 1I2B UPG 0.01728 0.40148 3.34728
54 1I2B NAD 0.01728 0.40148 3.34728
55 2G50 PYR 0.01967 0.40044 3.34728
56 1I52 CTP 0.002556 0.41026 3.38983
57 3K9W 4PS 0.03536 0.40639 3.74332
58 3K9W ADE 0.03536 0.40639 3.74332
59 3FC2 IBI 0.0002098 0.44908 3.76569
60 2Z9V PXM 0.0007432 0.44794 3.76569
61 4HA6 FAD 0.005831 0.41164 3.76569
62 1JIL 485 0.0009314 0.41046 3.76569
63 3ZV6 4HB 0.006981 0.40775 3.76569
64 2NLI FMN 0.01062 0.40676 3.76569
65 2NLI LAC 0.01062 0.40676 3.76569
66 4PVV HO4 0.006375 0.4053 3.76569
67 2XK9 XK9 0.005572 0.40308 3.76569
68 1RHC F42 ACN 0.004125 0.40282 3.76569
69 3GE7 AFQ 0.006109 0.40044 3.76569
70 3KO8 NAD 0.001553 0.42074 3.84615
71 1G8S MET 0.01594 0.40258 3.91304
72 3D3W NAP 0.0001154 0.46302 4.1841
73 1EP2 FMN 0.000317 0.43949 4.1841
74 1EP2 ORO 0.0005997 0.43839 4.1841
75 3DNT ATP 0.000862 0.41739 4.1841
76 2E2R 2OH 0.003108 0.41234 4.1841
77 1V6A TRE 0.007349 0.41195 4.1841
78 1LC8 33P 0.001822 0.4111 4.1841
79 3DGB MUC 0.003672 0.40446 4.1841
80 1SB8 NAD 0.01151 0.40382 4.1841
81 2ZB3 NDP 0.003558 0.40375 4.1841
82 1V35 NAI 0.008571 0.40346 4.1841
83 1HV9 COA 0.01294 0.40187 4.1841
84 1DJ9 KAM 0.002829 0.40123 4.1841
85 1JQI CAA 0.002838 0.40119 4.1841
86 1SS4 GSH 0.0004352 0.52135 4.57516
87 1SS4 CIT 0.02518 0.43919 4.57516
88 3P3N AKG 0.0008924 0.45822 4.60251
89 2RGH FAD 0.003932 0.41518 4.60251
90 1FIQ SAL 0.002912 0.41088 4.60251
91 1FIQ MTE 0.002457 0.41088 4.60251
92 1HDR NAD 0.01217 0.40368 4.60251
93 2WA4 069 0.004683 0.40048 4.60251
94 3DER ALA LYS 0.001846 0.40042 4.60251
95 1NHZ 486 0.0005703 0.42169 5.02092
96 1YBH FAD 0.002901 0.41908 5.02092
97 1RZM E4P 0.01397 0.41078 5.02092
98 1SOW NAD 0.003129 0.40975 5.02092
99 4NPT 017 0.0003788 0.40035 5.05051
100 3S9K CIT 0.01177 0.44206 5.08475
101 2VEZ G6P 0.001366 0.42 5.26316
102 2VEZ ACO 0.001496 0.41714 5.26316
103 1WXI AMP 0.00231 0.42276 5.43933
104 2V7T SAH 0.01562 0.4191 5.43933
105 3SHR CMP 0.002399 0.41625 5.43933
106 4KQI RBZ 0.002611 0.41128 5.43933
107 4KQI NIO 0.002611 0.41128 5.43933
108 4AXD ANP 0.00612 0.40384 5.43933
109 2C31 TZD 0.02863 0.4018 5.43933
110 2C31 ADP 0.02778 0.4018 5.43933
111 4F8L GAL 0.00771 0.45428 5.51724
112 3ZPG 5GP 0.002253 0.46345 5.85774
113 3ICC NAP 0.000128 0.45989 5.85774
114 1R6D DAU 0.003526 0.42689 5.85774
115 3IAE D7K 0.001208 0.42332 5.85774
116 1M5B BN1 0.005669 0.4219 5.85774
117 1P72 ADP 0.001375 0.4213 5.85774
118 3WE0 FAD 0.004491 0.41593 5.85774
119 1H82 FAD 0.01396 0.4065 5.85774
120 1R6D NAD 0.01723 0.40081 5.85774
121 3F81 STT 0.003055 0.45684 6.01093
122 1TUV VK3 0.007187 0.43826 6.14035
123 2YC5 6BC 0.005778 0.40365 6.14035
124 1JYQ MAZ PTR PTM ASN 0.00842 0.41066 6.25
125 2J07 FAD 0.007658 0.41144 6.27615
126 2J07 HDF 0.007658 0.41144 6.27615
127 3F3E LEU 0.004387 0.41027 6.27615
128 2F2U M77 0.003576 0.40952 6.27615
129 4FWE FAD 0.009339 0.40389 6.27615
130 3WBF NAP 0.003588 0.40362 6.27615
131 2AMV BIN 0.01523 0.4007 6.27615
132 3VPD ANP 0.0005544 0.42014 6.69456
133 1Q3Q ANP 0.01608 0.40409 6.69456
134 1DR1 NAP 0.006551 0.40382 6.87831
135 1DR1 HBI 0.006551 0.40382 6.87831
136 3EAU NDP 0.01034 0.42254 7.11297
137 1DLJ UGA 0.01154 0.40537 7.11297
138 1D09 PAL 0.03595 0.40962 7.18954
139 1NNU TCT 0.005296 0.43551 7.42358
140 1NNU NAD 0.005296 0.43551 7.42358
141 4TMK T5A 0.03291 0.41238 7.51174
142 1UXG FUM 0.004125 0.41233 7.53138
143 1UXG NAD 0.004125 0.41233 7.53138
144 1D6H COA 0.006585 0.40964 7.53138
145 1RP0 AHZ 0.01977 0.4067 7.53138
146 3BY8 MLT 0.0002684 0.48988 7.74648
147 4IAE 1DX 0.01508 0.40047 7.93651
148 3CIP ATP 0.004105 0.41645 7.94979
149 4G1V FAD 0.002662 0.40679 7.94979
150 4C12 ADP 0.001271 0.44406 8.3682
151 3UR0 SVR 0.001 0.4416 8.3682
152 3PNL ADP 0.002375 0.40045 8.3682
153 2BJK NAD 0.009621 0.41033 8.78661
154 2J7T 274 0.002981 0.40648 8.78661
155 4G87 UD1 0.01107 0.40324 8.78661
156 2E1A MSE 0.003376 0.41545 9.33333
157 4O8A FAD 0.002374 0.41277 9.62343
158 3IU9 T07 0.01116 0.41102 9.62343
159 2ORV 4TA 0.002392 0.40376 9.82906
160 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.002686 0.42137 10.0418
161 4PLG NAI 0.004891 0.40852 10.0418
162 4PLG OXM 0.004891 0.40852 10.0418
163 4CS4 AXZ 0.01127 0.40078 10.0418
164 2I4O ATP 0.0002616 0.40005 10.0418
165 1XVV CCQ 0.003203 0.41747 10.4603
166 4DQ2 BTX 0.002111 0.41182 10.4603
167 2PT9 2MH 0.003258 0.41159 10.5919
168 2PT9 S4M 0.003181 0.40105 10.5919
169 1GSA GSH 0.001579 0.43105 10.8787
170 2R40 EPH 0.001572 0.41852 11.2971
171 2QIA U20 0.01203 0.40655 11.7155
172 2I7C AAT 0.003348 0.40994 12.0141
173 2QLX RM4 0.01797 0.40571 12.037
174 1Q0H FOM 0.003796 0.42054 12.1339
175 1Q0H NDP 0.005187 0.41712 12.1339
176 4LWA Q13 0.006225 0.40671 12.1339
177 2YVF NAD 0.01139 0.41267 12.9707
178 2YVF FAD 0.01097 0.41267 12.9707
179 1RBO CAP 0.003006 0.46082 13.3891
180 3FC4 EDO 0.008705 0.4124 13.8075
181 2V5E SCR 0.006256 0.44971 13.8614
182 3EE4 MYR 0.001675 0.40379 14.2259
183 3UXL CFI 0.003668 0.41732 15.0628
184 1G0N NDP 0.002406 0.42102 15.8996
185 1G0N PHH 0.003893 0.41635 15.8996
186 1WVC CTP 0.01737 0.41529 16.7364
187 3PLN U5P 0.002021 0.42997 17.5732
188 1FW1 GSH 0.0005268 0.4309 22.2222
189 1KYV RBF 0.001112 0.40144 23.8994
190 1Z44 NPO 0.03357 0.419 28.8703
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