Receptor
PDB id Resolution Class Description Source Keywords
2B4G 1.95 Å EC: 1.3.5.2 DIHYDROOROTATE DEHYDROGENASE TRYPANOSOMA BRUCEI STRUCTURAL GENOMICS PSI PROTEIN STRUCTURE INITIATIVE STRUGENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM SGPP OXIDOREDU
Ref.: CHARACTERIZATION OF TRYPANOSOMA BRUCEI DIHYDROOROTA DEHYDROGENASE AS A POSSIBLE DRUG TARGET; STRUCTURAL AND RNAI STUDIES MOL.MICROBIOL. V. 68 37 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BR A:1411;
A:1412;
A:1414;
A:1415;
B:1413;
B:2410;
C:3410;
C:3411;
C:4410;
D:4411;
D:4412;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
79.904 Br [Br-]
FMN A:1400;
B:2400;
C:3400;
D:4400;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
GOL A:1401;
A:1403;
C:3401;
D:4401;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
ORO A:1399;
B:2399;
C:3399;
D:4399;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
156.096 C5 H4 N2 O4 C1=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2B4G 1.95 Å EC: 1.3.5.2 DIHYDROOROTATE DEHYDROGENASE TRYPANOSOMA BRUCEI STRUCTURAL GENOMICS PSI PROTEIN STRUCTURE INITIATIVE STRUGENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM SGPP OXIDOREDU
Ref.: CHARACTERIZATION OF TRYPANOSOMA BRUCEI DIHYDROOROTA DEHYDROGENASE AS A POSSIBLE DRUG TARGET; STRUCTURAL AND RNAI STUDIES MOL.MICROBIOL. V. 68 37 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2B4G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3C3N - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 2E6D - FUM C4 H4 O4 C(=C/C(=O)....
3 4WZH - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1JQX Kd = 95 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
5 1JQV Kd = 117 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
6 2DOR - ORO C5 H4 N2 O4 C1=C(NC(=O....
7 1DOR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1JRB Kd = 1450 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
9 1JUE - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 1OVD Kd = 7.6 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
11 1JRC Kd = 44 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
12 2BX7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 2BSL Kd = 8 uM DHB C7 H6 O4 c1cc(c(cc1....
14 1JUB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 4EF8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 3MJY Ki = 82.8 uM IJZ C5 H5 N3 O4 C1(=C(NC(=....
17 4EF9 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 3MHU Ki = 212.93 uM EJZ C5 H3 N3 O6 C1(=C(NC(=....
19 3TQ0 - FUM C4 H4 O4 C(=C/C(=O)....
20 2B4G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3C3N - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 2E6D - FUM C4 H4 O4 C(=C/C(=O)....
3 4WZH - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1JQX Kd = 95 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
5 1JQV Kd = 117 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
6 2DOR - ORO C5 H4 N2 O4 C1=C(NC(=O....
7 1DOR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1JRB Kd = 1450 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
9 1JUE - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 1OVD Kd = 7.6 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
11 1JRC Kd = 44 uM ORO C5 H4 N2 O4 C1=C(NC(=O....
12 2BX7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 2BSL Kd = 8 uM DHB C7 H6 O4 c1cc(c(cc1....
14 1JUB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 4EF8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 3MJY Ki = 82.8 uM IJZ C5 H5 N3 O4 C1(=C(NC(=....
17 4EF9 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 3MHU Ki = 212.93 uM EJZ C5 H3 N3 O6 C1(=C(NC(=....
19 3TQ0 - FUM C4 H4 O4 C(=C/C(=O)....
20 2B4G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
21 3OIX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 DLZ 0.404494 0.782051
Ligand no: 2; Ligand: ORO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 ORO 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2B4G; Ligand: ORO; Similar sites found: 20
This union binding pocket(no: 1) in the query (biounit: 2b4g.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TKA SAM 0.02922 0.40037 2.2082
2 1K0D GSH 0.02002 0.40174 2.30769
3 1PHP ADP 0.03173 0.40005 2.83912
4 4KCF AKM 0.02822 0.40421 3.15457
5 2Z48 A2G 0.006455 0.41122 3.47003
6 2Z48 NGA 0.005735 0.40218 3.47003
7 3G6K FAD 0.004777 0.4558 3.57143
8 3G6K POP 0.005189 0.45262 3.57143
9 4IF4 BEF 0.012 0.40071 4.32692
10 3P13 RIP 0.009557 0.4048 4.86111
11 3BC1 GNP 0.0214 0.41196 5.12821
12 3EYA FAD 0.0288 0.41706 6.62461
13 5EYP GTP 0.02302 0.41305 7.88644
14 1Q19 APC 0.01483 0.41564 9.46372
15 1YNH SUO 0.009744 0.42986 12.3028
16 5K2M ADP 0.01546 0.41788 13.2075
17 1YZQ GNP 0.03589 0.40148 15.8824
18 1F76 ORO 0.000000001194 0.65551 36.2776
19 1F76 FMN 0.01296 0.42485 36.2776
20 1EP2 ORO 0.00000004906 0.41985 45.0161
Pocket No.: 2; Query (leader) PDB : 2B4G; Ligand: FMN; Similar sites found: 135
This union binding pocket(no: 2) in the query (biounit: 2b4g.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1P4C FMN 0.0006505 0.43781 1.57729
2 4O48 ASP 0.01757 0.42008 1.57729
3 3QH2 3NM 0.0005513 0.49826 1.80995
4 4XP7 FNR 0.000003317 0.48177 1.89274
5 4PPF FLC 0.01327 0.4316 1.89274
6 1PS9 FMN 0.0007032 0.41538 1.89274
7 5THY SAH 0.007876 0.40306 1.89274
8 5OCS FMN 0.0001308 0.48879 2.2082
9 3W9Z FMN 0.00003116 0.45229 2.2082
10 4YRD 3IT 0.02416 0.4141 2.2082
11 2OG2 MLI 0.02187 0.41277 2.2082
12 4IXH IMP 0.003527 0.41166 2.2082
13 2AJ4 GLA 0.03017 0.40681 2.2082
14 3GLC R5P 0.003758 0.43979 2.37288
15 2YPI PGA 0.006676 0.43193 2.42915
16 4M26 AKG 0.02923 0.40883 2.52366
17 2PW0 TRC 0.03618 0.40127 2.52366
18 4JIQ FMN 0.00001483 0.50017 2.83912
19 4JIQ 1L5 0.00001483 0.50017 2.83912
20 1OYB FMN 0.00004246 0.49077 2.83912
21 1VHN FMN 0.0006669 0.47636 2.83912
22 1OYB HBA 0.00009208 0.46479 2.83912
23 2R14 FMN 0.000312 0.44411 2.83912
24 2R14 TXD 0.0004495 0.41769 2.83912
25 3B00 16A 0.02421 0.40021 2.94118
26 4CW5 FMN 0.0004368 0.40977 3.15457
27 1ME8 RVP 0.001634 0.42825 3.47003
28 1DJN FMN 0.001741 0.40582 3.47003
29 1YQC GLV 0.02668 0.40364 3.52941
30 1QDS PGA 0.001677 0.46188 3.58566
31 5EYW PGA 0.002886 0.45516 3.61446
32 3EXS 5RP 0.005557 0.43591 3.61991
33 1M5W DXP 0.0378 0.40159 3.7037
34 1KBJ FMN 0.00001393 0.49194 3.78549
35 1KBI PYR 0.00002634 0.48599 3.78549
36 4I9A NCN 0.002333 0.4369 3.81944
37 1SW0 PGA 0.003062 0.44413 4.03226
38 4M5P FMN 0.00005783 0.4945 4.10095
39 5DKK FMN 0.01143 0.40215 4.13793
40 4K7O EKZ 0.008576 0.43486 4.16667
41 3NZ1 3NY 0.002159 0.46975 4.21456
42 5HX1 UMP 0.04065 0.40063 4.34783
43 4UTU LRY 0.007838 0.42023 4.36681
44 4UTW RFW 0.01022 0.41108 4.36681
45 2Z6I FMN 0.000138 0.47392 4.4164
46 4A3U FMN 0.00002052 0.46515 4.4164
47 4IEE AGS 0.02042 0.41156 4.4164
48 4PEG 5GP 0.03783 0.40667 4.4164
49 1ZN7 HSX 0.01508 0.41421 4.44444
50 4Q4K FMN 0.00009145 0.46125 4.73186
51 2Z6J FMN 0.0001463 0.44568 4.73186
52 1ONX ASP 0.02022 0.41603 4.73186
53 3B9Q MLI 0.02964 0.41219 4.96689
54 4JGT PYR 0.01281 0.41029 5.01672
55 2HSA FMN 0.00002673 0.47298 5.04732
56 1OX5 1PR 0.001506 0.41266 5.04732
57 1FRW GTP 0.006632 0.41985 5.15464
58 1WHT BZS 0.0295 0.40576 5.22876
59 2DBX GLU 0.002939 0.4629 5.26316
60 2RDT 2RD 0.00003068 0.49057 5.36278
61 2RDT FMN 0.00001559 0.49024 5.36278
62 1SQK LAR 0.01635 0.41244 5.36278
63 4B1V LAB 0.02748 0.40108 5.36278
64 5A5W GUO 0.003933 0.41597 5.5336
65 2XBL M7P 0.0108 0.40996 5.55556
66 4YMZ 13P 0.00215 0.4617 5.57769
67 2ZTG A5A 0.006434 0.41681 5.67823
68 1BWV CAP 0.01075 0.40335 5.67823
69 5CSS G3P 0.0007401 0.48537 5.75221
70 2C6Q IMP 0.002653 0.41367 5.99369
71 1OFD AKG 0.0004364 0.4108 5.99369
72 1OFD FMN 0.0005128 0.4012 5.99369
73 1PTR PRB 0.02485 0.41322 6
74 1D1Q 4NP 0.03767 0.40509 6.21118
75 4BQS K2Q 0.02504 0.40698 6.25
76 2GJN FMN 0.0004117 0.44285 6.30915
77 2GJN NIS 0.0004501 0.43303 6.30915
78 2V68 CAP 0.005464 0.41311 6.30915
79 2V67 CAP 0.005788 0.4088 6.30915
80 1UZH CAP 0.007447 0.4041 6.30915
81 2FJK 13P 0.007405 0.42968 6.55738
82 4PU6 ASP 0.01208 0.42785 6.59898
83 4N02 FNR 0.000005903 0.50233 6.62461
84 2GOU FMN 0.0002846 0.45501 6.62461
85 3BW2 FMN 0.00007097 0.45189 6.62461
86 2BTM PGA 0.00259 0.45756 6.74603
87 2F6U CIT 0.01711 0.41988 6.83761
88 2Q3R FMN 0.000004203 0.48347 6.94006
89 1ICP FMN 0.0000513 0.47831 6.94006
90 3ATY FMN 0.00004007 0.46971 6.94006
91 3HF3 FMN 0.00009687 0.44617 6.94006
92 2NLI FMN 0.0003641 0.43015 6.94006
93 2NLI LAC 0.0008668 0.42839 6.94006
94 4J25 OGA 0.03175 0.40164 6.9869
95 4RYV ZEA 0.01332 0.41691 7.09677
96 2YIP YIO 0.03091 0.40485 7.24638
97 3B0P FMN 0.000003837 0.57049 7.25552
98 3O2K DST 0.01166 0.42867 7.25552
99 4V15 PLP 0.0222 0.40206 7.25552
100 2Y88 2ER 0.002938 0.41673 7.37705
101 1SQL GUN 0.0313 0.40174 7.53425
102 4B1L FRU 0.02167 0.41028 7.87879
103 4EWN 0VR 0.00632 0.42083 7.90514
104 4TMC FMN 0.00001454 0.51495 8.20189
105 4TMC HBA 0.00003792 0.4883 8.20189
106 1VYP FMN 0.00008307 0.4622 8.20189
107 1VYP TNF 0.00006725 0.46129 8.20189
108 1Y13 BIO 0.02013 0.41188 8.28729
109 1T9D P22 0.03399 0.40405 8.51735
110 1AL8 FMN 0.00001917 0.505 9.14826
111 1AL8 DHP 0.0002193 0.4339 9.14826
112 4NAE 1GP 0.00002858 0.5771 9.33333
113 3KRU FMN 0.0001462 0.46513 9.46372
114 1Z44 FMN 0.00002021 0.54341 10.4101
115 1Z41 FMN 0.00001866 0.53855 10.4101
116 1Z42 FMN 0.00005791 0.52801 10.4101
117 1Z48 FMN 0.00001823 0.44528 10.4101
118 3CR3 ADP 0.01243 0.40051 10.7438
119 3OVR 5SP 0.002892 0.41841 10.9649
120 3OQJ 3CX 0.02425 0.40382 11.284
121 4QNW FMN 0.00002308 0.51157 11.3565
122 1IR2 CAP 0.007694 0.4035 11.4286
123 2Q3O FMN 0.00005788 0.48976 11.6719
124 4NPT 017 0.0225 0.40546 12.1212
125 2ZRU FMN 0.000161 0.41317 13.5647
126 3N9R TD3 0.01018 0.42276 13.6808
127 5TCI MLI 0.002427 0.46742 16.3043
128 1TB3 FMN 0.00001868 0.4974 17.9811
129 3H0L ADP 0.0256 0.40263 18.0851
130 3IWD M2T 0.03348 0.40486 20.5882
131 1F76 FMN 0.000000000007205 0.73218 36.2776
132 1GTE FMN 0.000000000001884 0.67376 41.9558
133 1GTE IUR 0.000000000001884 0.67376 41.9558
134 1EP2 FMN 0.0000000000002205 0.78491 45.0161
135 1EP2 ORO 0.0000000000006498 0.68943 45.0161
Pocket No.: 3; Query (leader) PDB : 2B4G; Ligand: FMN; 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: 2b4g.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2B4G; Ligand: ORO; 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: 2b4g.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2B4G; Ligand: ORO; Similar sites found: 5
This union binding pocket(no: 5) in the query (biounit: 2b4g.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JA9 NDP 0.02124 0.42103 1.82482
2 3ZQ6 ADP ALF 0.03718 0.40067 1.89274
3 5BSH PRO 0.04951 0.40108 2.88809
4 3TNF GNP 0.02632 0.40996 9.77011
5 1G51 AMO 0.03805 0.40143 9.77918
Pocket No.: 6; Query (leader) PDB : 2B4G; Ligand: ORO; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2b4g.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2B4G; Ligand: FMN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2b4g.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2B4G; Ligand: FMN; Similar sites found: 25
This union binding pocket(no: 8) in the query (biounit: 2b4g.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5KBE IPH 0.02062 0.41559 2.18341
2 4JLZ UTP 0.04843 0.40623 2.52366
3 2G50 PYR 0.03132 0.40271 2.52366
4 1H5R THM 0.02838 0.40037 3.41297
5 5B3A 0JO 0.005735 0.4059 3.47003
6 2GMP NAG MAN 0.01754 0.4222 3.57143
7 3GAY P6T 0.006914 0.40864 3.78549
8 4CUB GAL NAG 0.02433 0.40894 3.82514
9 4XFM THE 0.02379 0.41149 4.10095
10 4D52 GXL 0.03565 0.40359 4.44444
11 2HXW FLC 0.03669 0.40228 4.64135
12 1YBH P22 0.01915 0.40898 5.67823
13 1IGW PYR 0.03239 0.40238 5.99369
14 5L2R LMR 0.02235 0.40561 6.30915
15 1TZJ A3B 0.04121 0.4004 6.30915
16 4C1W SLT 0.007702 0.43394 6.38298
17 3BF1 PAU 0.02417 0.40025 7.22892
18 1IR1 CAP 0.01005 0.40151 7.31707
19 4UP4 NDG 0.00424 0.45468 7.88644
20 4UP4 NAG 0.00424 0.45468 7.88644
21 4GV8 DUP 0.01271 0.40666 8.87574
22 2CXG GLC GLC 0.03653 0.4056 9.14826
23 5CLO NS8 0.03758 0.4036 10.1695
24 5D4Y BXP 0.03397 0.40406 10.7256
25 3WCS MAN NAG 0.03752 0.40176 14.1732
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