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Receptor
PDB id Resolution Class Description Source Keywords
1X1Z 1.45 Å EC: 4.1.1.23 OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ODCASE) COMPLEXED (PRODUCED FROM 6-CYANOUMP) METHANOTHERMOBACTER THERMAUTOTROPHICUSORGANISM_TAXID: 145262 OROTIDINE 5-prime -MONOPHOSPHATE DECARBOXYLASE (ODCASE) BARBITURIRIBOSYL 5-prime -MONOPHOSPHATE (BMP) 6-CYANOUMP LYASE
Ref.: AN UNPRECEDENTED TWIST TO ODCASE CATALYTIC ACTIVITY J.AM.CHEM.SOC. V. 127 15048 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BMP A:301;
A:302;
Valid;
Valid;
none;
none;
Ki = 8.8 pM
340.181 C9 H13 N2 O10 P C1=C(...
GOL A:311;
A:312;
A:314;
B:313;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1X1Z 1.45 Å EC: 4.1.1.23 OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ODCASE) COMPLEXED (PRODUCED FROM 6-CYANOUMP) METHANOTHERMOBACTER THERMAUTOTROPHICUSORGANISM_TAXID: 145262 OROTIDINE 5-prime -MONOPHOSPHATE DECARBOXYLASE (ODCASE) BARBITURIRIBOSYL 5-prime -MONOPHOSPHATE (BMP) 6-CYANOUMP LYASE
Ref.: AN UNPRECEDENTED TWIST TO ODCASE CATALYTIC ACTIVITY J.AM.CHEM.SOC. V. 127 15048 2005
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2ZZ5 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
2 1KLZ - U C9 H13 N2 O9 P C1=CN(C(=O....
3 3WJZ - NUP C9 H14 N3 O9 P C1=C(N(C(=....
4 1X1Z Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
5 2ZZ2 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
70% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3V1P - BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3G24 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 1LOS Ki = 64 nM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
4 3NQG - BMP C9 H13 N2 O10 P C1=C(N(C(=....
5 3NQD - BMP C9 H13 N2 O10 P C1=C(N(C(=....
6 3LHY - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
7 3LTS - BMP C9 H13 N2 O10 P C1=C(N(C(=....
8 3G1X - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1KM0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
10 3WJX Ki = 840 nM NUP C9 H14 N3 O9 P C1=C(N(C(=....
11 1LP6 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
12 3LLF - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
13 3G1D - U C9 H13 N2 O9 P C1=CN(C(=O....
14 3LHT - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
15 3NQE - BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3WK1 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
17 1KM3 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 3LV5 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
19 3LHW - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
20 1KM1 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
21 3LV6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
22 3G1F Ki = 100 uM 2OM C10 H15 N2 O11 P C1[C@@H](N....
23 3M1Z - BMP C9 H13 N2 O10 P C1=C(N(C(=....
24 3W07 Kd = 420 uM U5P C9 H13 N2 O9 P C1=CN(C(=O....
25 3PBU - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
26 1LOR Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
27 3NQC - BMP C9 H13 N2 O10 P C1=C(N(C(=....
28 3LHZ - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
29 1KM2 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
30 3PC0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
31 3WK2 - O7M C11 H15 N2 O11 P COC(=O)C1=....
32 3PBY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
33 3LI0 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
34 1KM4 - U C9 H13 N2 O9 P C1=CN(C(=O....
35 3LHU - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
36 3G22 - U C9 H13 N2 O9 P C1=CN(C(=O....
37 2ZZ1 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
38 4GC4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
39 4FX8 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
40 3LI1 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
41 1KLY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
42 3G1V - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
43 1DVJ Ki = 0.51 mM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
44 3LTY - BMP C9 H13 N2 O10 P C1=C(N(C(=....
45 3WJY - NUP C9 H14 N3 O9 P C1=C(N(C(=....
46 1KM5 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
47 3PBW - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
48 3WK0 - O7M C11 H15 N2 O11 P COC(=O)C1=....
49 2ZZ7 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
50 3NQM - BMP C9 H13 N2 O10 P C1=C(N(C(=....
51 4FX6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
52 3G1H - H2U C9 H15 N2 O9 P C1CN(C(=O)....
53 4FXR - BMP C9 H13 N2 O10 P C1=C(N(C(=....
54 1KM6 - OMP C10 H13 N2 O11 P C1=C(N(C(=....
55 3LTP - BMP C9 H13 N2 O10 P C1=C(N(C(=....
56 3WJW Ki = 134 uM U6M C10 H15 N2 O9 P CC1=CC(=O)....
57 3LLD - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
58 3NQF - BMP C9 H13 N2 O10 P C1=C(N(C(=....
59 1LOQ Ki = 0.2 mM U C9 H13 N2 O9 P C1=CN(C(=O....
60 3G1A - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
61 3PBV - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
62 3WK3 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
63 3LHV - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
64 1LOL Ki = 0.41 uM XMP C10 H14 N4 O9 P c1[nH+]c2c....
65 2ZZ5 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
66 1KLZ - U C9 H13 N2 O9 P C1=CN(C(=O....
67 3WJZ - NUP C9 H14 N3 O9 P C1=C(N(C(=....
68 1X1Z Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
69 2ZZ2 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
50% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3V1P - BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3G24 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 1LOS Ki = 64 nM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
4 3NQG - BMP C9 H13 N2 O10 P C1=C(N(C(=....
5 3NQD - BMP C9 H13 N2 O10 P C1=C(N(C(=....
6 3LHY - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
7 3LTS - BMP C9 H13 N2 O10 P C1=C(N(C(=....
8 3G1X - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1KM0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
10 3WJX Ki = 840 nM NUP C9 H14 N3 O9 P C1=C(N(C(=....
11 1LP6 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
12 3LLF - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
13 3G1D - U C9 H13 N2 O9 P C1=CN(C(=O....
14 3LHT - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
15 3NQE - BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3WK1 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
17 1KM3 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 3LV5 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
19 3LHW - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
20 1KM1 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
21 3LV6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
22 3G1F Ki = 100 uM 2OM C10 H15 N2 O11 P C1[C@@H](N....
23 3M1Z - BMP C9 H13 N2 O10 P C1=C(N(C(=....
24 3W07 Kd = 420 uM U5P C9 H13 N2 O9 P C1=CN(C(=O....
25 3PBU - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
26 1LOR Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
27 3NQC - BMP C9 H13 N2 O10 P C1=C(N(C(=....
28 3LHZ - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
29 1KM2 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
30 3PC0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
31 3WK2 - O7M C11 H15 N2 O11 P COC(=O)C1=....
32 3PBY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
33 3LI0 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
34 1KM4 - U C9 H13 N2 O9 P C1=CN(C(=O....
35 3LHU - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
36 3G22 - U C9 H13 N2 O9 P C1=CN(C(=O....
37 2ZZ1 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
38 4GC4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
39 4FX8 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
40 3LI1 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
41 1KLY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
42 3G1V - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
43 1DVJ Ki = 0.51 mM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
44 3LTY - BMP C9 H13 N2 O10 P C1=C(N(C(=....
45 3WJY - NUP C9 H14 N3 O9 P C1=C(N(C(=....
46 1KM5 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
47 3PBW - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
48 3WK0 - O7M C11 H15 N2 O11 P COC(=O)C1=....
49 2ZZ7 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
50 3NQM - BMP C9 H13 N2 O10 P C1=C(N(C(=....
51 4FX6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
52 3G1H - H2U C9 H15 N2 O9 P C1CN(C(=O)....
53 4FXR - BMP C9 H13 N2 O10 P C1=C(N(C(=....
54 1KM6 - OMP C10 H13 N2 O11 P C1=C(N(C(=....
55 3LTP - BMP C9 H13 N2 O10 P C1=C(N(C(=....
56 3WJW Ki = 134 uM U6M C10 H15 N2 O9 P CC1=CC(=O)....
57 3LLD - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
58 3NQF - BMP C9 H13 N2 O10 P C1=C(N(C(=....
59 1LOQ Ki = 0.2 mM U C9 H13 N2 O9 P C1=CN(C(=O....
60 3G1A - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
61 3PBV - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
62 3WK3 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
63 3LHV - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
64 1LOL Ki = 0.41 uM XMP C10 H14 N4 O9 P c1[nH+]c2c....
65 2ZZ5 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
66 1KLZ - U C9 H13 N2 O9 P C1=CN(C(=O....
67 3WJZ - NUP C9 H14 N3 O9 P C1=C(N(C(=....
68 1X1Z Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
69 2ZZ2 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BMP; Similar ligands found: 32
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 U 0.513889 0.955224
14 UP6 0.513889 0.847222
15 U5P 0.513889 0.955224
16 8OP 0.5125 0.815789
17 8GM 0.4875 0.868421
18 H2U 0.479452 0.873239
19 5FU 0.466667 0.915493
20 5BU 0.454545 0.915493
21 2OM 0.448718 0.885714
22 CNU 0.4375 0.928571
23 TKW 0.417722 0.915493
24 H6Y 0.417582 0.828947
25 8OD 0.41573 0.828947
26 CAR 0.405063 0.901408
27 C5P 0.405063 0.901408
28 C 0.405063 0.901408
29 UTP 0.404762 0.970149
30 UDP 0.402439 0.970149
31 44P 0.4 0.928571
32 ICR 0.4 0.821918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1X1Z; Ligand: BMP; Similar sites found with APoc: 124
This union binding pocket(no: 1) in the query (biounit: 1x1z.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 2W5P CL8 None
2 6BVE PGA 1.63265
3 2BTM PGA 1.98413
4 1O68 KIV 1.98413
5 4L80 OXL 1.98413
6 2BMB PMM 2.38095
7 5WAN FMN 2.38095
8 6ACS CIT 2.77778
9 3H22 B53 2.77778
10 4TMC FMN 2.77778
11 5GJO PLP 3.1746
12 1XG4 ICT 3.1746
13 1JQN DCO 3.1746
14 4TO8 FLC 3.1746
15 5YJS SAL 3.1746
16 5OCS FMN 3.1746
17 1PMO PLR 3.1746
18 4CW5 FMN 3.1746
19 1QDS PGA 3.18725
20 2YPI PGA 3.23887
21 5WS9 OXL 3.57143
22 4JEJ 1GP 3.68852
23 1NC2 DOE 3.72093
24 1Z44 FMN 3.84615
25 1Z48 FMN 3.84615
26 1Z42 FMN 3.84615
27 1Z41 FMN 3.84615
28 4WGF HX2 3.90244
29 5EXA 5SO 3.91304
30 3OVR 5SP 3.94737
31 1FDJ 13P 3.96825
32 3TAO PGH 3.96825
33 3VKC FPQ 3.96825
34 2WW5 CHT 3.96825
35 3NZ1 3NY 3.96825
36 4A3U FMN 3.96825
37 6BYF CIT 4.11765
38 5AHN IMP 4.29448
39 5EYW PGA 4.36508
40 4J51 N75 4.36508
41 4XH0 ADP 4.36508
42 4V15 PLP 4.36508
43 5YSN 5AD 4.36508
44 4IA6 EIC 4.36508
45 5WGG SAM 4.36508
46 2GVJ DGB 4.36508
47 1LBF 137 4.45344
48 3QH2 3NM 4.52489
49 3N9R TD3 4.7619
50 4K37 SAM 4.7619
51 4K38 SAM 4.7619
52 3E3U NVC 4.7619
53 3GLC R5P 5.15873
54 1GVF PGH 5.15873
55 1L5Y BEF 5.16129
56 1LYX PGA 5.24194
57 1VKF CIT 5.31915
58 1G51 AMP 5.55556
59 1S5O 152 5.55556
60 3HQP OXL 5.55556
61 6BKA FMN 5.55556
62 4EWN 0VR 5.95238
63 1JT2 FER 5.95238
64 4XP7 FNR 5.95238
65 4YMZ 13P 5.9761
66 1Z0N BCD 6.25
67 3W9Z FMN 6.34921
68 2Q3R FMN 6.34921
69 2V67 CAP 6.34921
70 1UZD CAP 6.34921
71 1IR2 CAP 6.34921
72 2V6A CAP 6.34921
73 2V68 CAP 6.34921
74 2Q3O FMN 6.74603
75 2G50 PYR 6.74603
76 1QPR PPC 6.74603
77 4B5W PYR 7.14286
78 4RW3 IPD 7.14286
79 1TUF AZ1 7.14286
80 1KUJ MMA 7.5188
81 2FJK 13P 7.53968
82 2OVW CBI 7.53968
83 4BI7 PGA 7.93651
84 1SW0 PGA 8.06452
85 1W8S FBP 8.33333
86 1O5Q PYR 8.33333
87 1NJJ ORX 8.33333
88 4IF4 BEF 8.65385
89 4I9A NCN 9.12698
90 4IP7 FLC 9.52381
91 2WQ4 SFU 9.61539
92 3A8H TAY 9.66184
93 1JCM 137 9.92064
94 4LUT DCS 10.3175
95 3NNT DQA 10.3175
96 4QPL V3L 10.3226
97 4KCT PYR 10.7143
98 4UTU LRY 10.917
99 4UTW RFW 10.917
100 2PLK P3D 11.1111
101 3CTL S6P 11.2554
102 2FKA BEF 11.6279
103 3WIR BGC 11.9048
104 2F6U CIT 11.9658
105 1QFT HSM 12
106 4NAE 1GP 12.3016
107 2R42 FPS 12.3016
108 1RBL CAP 13.0952
109 1TRD PGH 13.2
110 3HRD NIO 13.75
111 5TCI MLI 14.6825
112 3B0P FMN 15.0794
113 1P7T PYR 15.4762
114 4QNW FMN 16.6667
115 2Y5S 78H 17.8571
116 4IXH IMP 19.4444
117 2OO0 PLP 20.6349
118 5CSS G3P 20.7965
119 1Q6O LG6 25.9259
120 1M5W DXP 27.1605
121 2FLI DX5 31.3636
122 1UJP CIT 36.9048
123 3EXS 5RP 40.2715
124 2FFC U5P 40.4762
Pocket No.: 2; Query (leader) PDB : 1X1Z; Ligand: BMP; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 1x1z.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 1DZK PRZ None
2 2WW2 SWA 3.96825
3 4K39 SAM 4.7619
4 1SGJ OAA 5.6338
5 2O1O RIS 6.34921
6 3VSV XYP 7.14286
7 2C49 ADN 7.14286
8 1EYE PMM 7.93651
9 2WD7 VGD 8.73016
10 2OEM 1AE 9.52381
11 4GGZ BTN 10.4348
12 5BRP PNG 10.7143
13 1D8C GLV 15.0794
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