Receptor
PDB id Resolution Class Description Source Keywords
2ZRU 2 Å EC: 5.3.3.2 CRYSTAL STRUCTURE OF SULFOLOBUS SHIBATAE ISOPENTENYL DIPHOSP ISOMERASE IN COMPLEX WITH FMN SULFOLOBUS SHIBATAE TYPE 2 IDI FMN ISOPENTENYL DIPHOSPHATE ISOMERASE FLAVOPRISOMERASE ISOPRENE BIOSYNTHESIS NADP
Ref.: NEW ROLE OF FLAVIN AS A GENERAL ACID-BASE CATALYST REDOX FUNCTION IN TYPE 2 ISOPENTENYL-DIPHOSPHATE IS J.BIOL.CHEM. V. 284 9160 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:669;
B:669;
C:669;
D:669;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 467 nM
456.344 C17 H21 N4 O9 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZRU 2 Å EC: 5.3.3.2 CRYSTAL STRUCTURE OF SULFOLOBUS SHIBATAE ISOPENTENYL DIPHOSP ISOMERASE IN COMPLEX WITH FMN SULFOLOBUS SHIBATAE TYPE 2 IDI FMN ISOPENTENYL DIPHOSPHATE ISOMERASE FLAVOPRISOMERASE ISOPRENE BIOSYNTHESIS NADP
Ref.: NEW ROLE OF FLAVIN AS A GENERAL ACID-BASE CATALYST REDOX FUNCTION IN TYPE 2 ISOPENTENYL-DIPHOSPHATE IS J.BIOL.CHEM. V. 284 9160 2009
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ZRV - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
2 2ZRU Kd = 467 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3B05 - IPE C5 H12 O7 P2 CC(=C)CCO[....
4 3B06 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
5 2ZRW - IPE C5 H12 O7 P2 CC(=C)CCO[....
6 3VKJ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
7 3B04 - OOP C23 H35 N4 O17 P3 Cc1cc2c(cc....
8 3B03 - VNR C23 H35 N4 O16 P3 C/C=C(CCO[....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ZRV - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
2 2ZRU Kd = 467 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3B05 - IPE C5 H12 O7 P2 CC(=C)CCO[....
4 3B06 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
5 2ZRW - IPE C5 H12 O7 P2 CC(=C)CCO[....
6 3VKJ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
7 3B04 - OOP C23 H35 N4 O17 P3 Cc1cc2c(cc....
8 3B03 - VNR C23 H35 N4 O16 P3 C/C=C(CCO[....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ZRV - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
2 2ZRU Kd = 467 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3B05 - IPE C5 H12 O7 P2 CC(=C)CCO[....
4 3B06 - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
5 2ZRW - IPE C5 H12 O7 P2 CC(=C)CCO[....
6 3VKJ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
7 3B04 - OOP C23 H35 N4 O17 P3 Cc1cc2c(cc....
8 3B03 - VNR C23 H35 N4 O16 P3 C/C=C(CCO[....
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZRU; Ligand: FMN; 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: 2zru.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2ZRU; Ligand: FMN; 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: 2zru.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2ZRU; Ligand: FMN; Similar sites found: 111
This union binding pocket(no: 3) in the query (biounit: 2zru.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q3O FMN 0.000003381 0.45074 1.63043
2 5L9G MO0 0.009153 0.41746 1.7094
3 3HF3 FMN 0.000001952 0.45047 1.7192
4 4WZH FMN 0.0001054 0.48045 1.72911
5 2HSA FMN 0.000006703 0.46498 1.90217
6 2HZY DHJ 0.01203 0.41518 1.90217
7 2YGM GLA NAG GAL FUC 0.03234 0.41133 1.9774
8 5C79 PBU 0.02769 0.4168 2
9 3MJY IJZ 0.000118 0.43446 2.02312
10 3MJY FMN 0.000118 0.43446 2.02312
11 1OYB HBA 0.000003768 0.46358 2.17391
12 4QNW FMN 0.000001096 0.45882 2.17391
13 1OYB FMN 0.000002365 0.45545 2.17391
14 4M5P FMN 0.000002446 0.44176 2.17391
15 1VYP FMN 0.000007371 0.45053 2.1978
16 1VYP TNF 0.000009178 0.44346 2.1978
17 3KRU FMN 0.00002729 0.45421 2.33236
18 2Q3R FMN 0.0000007363 0.45749 2.44565
19 1OX5 1PR 0.002387 0.41876 2.44565
20 1Z42 FMN 0.000002004 0.61595 2.66272
21 1Z44 FMN 0.00000239 0.60424 2.66272
22 1Z48 FMN 0.000003085 0.42253 2.66272
23 1Z41 FMN 0.000002699 0.42207 2.66272
24 5UN9 NHT 0.03842 0.40028 2.71739
25 4A3U FMN 0.000002654 0.4466 2.7933
26 2FJK 13P 0.002855 0.46215 2.95082
27 5DG2 GAL GLC 0.02033 0.4109 2.96296
28 5O0X FAD 0.01413 0.4263 3.09278
29 1TMX BEZ 0.04433 0.40397 3.41297
30 1QY1 PRZ 0.009675 0.41017 3.44828
31 5OCS FMN 0.0000002548 0.6279 3.53261
32 1OFD FMN 0.000002115 0.50349 3.80435
33 1OFD AKG 0.000001569 0.50089 3.80435
34 1GTE IUR 0.00004501 0.46638 3.80435
35 1GTE FMN 0.00004501 0.4544 3.80435
36 1PS9 FMN 0.000001679 0.45397 3.80435
37 4YVN EBS 0.01524 0.4338 3.80435
38 4IGH 1EA 0.00007539 0.47875 4.07609
39 4IGH FMN 0.00007539 0.47875 4.07609
40 4IGH ORO 0.00007539 0.47875 4.07609
41 1UUO ORO 0.0001178 0.46345 4.07609
42 1UUO BRF 0.0001321 0.46345 4.07609
43 1DJN FMN 0.000009971 0.44449 4.07609
44 5HZ7 MLR 0.02163 0.4062 4.07609
45 1OJJ GLC GAL 0.0408 0.40591 4.07609
46 2X1L ADN 0.04023 0.40264 4.07609
47 4TMC FMN 0.000002607 0.56297 4.34783
48 4TMC HBA 0.000003061 0.54907 4.34783
49 4JIQ FMN 0.000006779 0.45128 4.34783
50 4JIQ 1L5 0.000006779 0.45128 4.34783
51 4P6C RES 0.01789 0.41361 4.62185
52 2Z6J FMN 0.00002424 0.4461 4.81928
53 2Z6I FMN 0.00002398 0.42098 4.81928
54 2R14 FMN 0.000006896 0.52469 4.8913
55 2R14 TXD 0.00001149 0.49905 4.8913
56 2BMZ XLM 0.006877 0.41678 4.96454
57 5M42 FMN 0.02587 0.40242 5.01792
58 4FOU C2E 0.03345 0.40335 5.12821
59 3B9Z CO2 0.04357 0.41195 5.16304
60 4TR9 ASP TRP ASN 0.03159 0.40132 5.16304
61 4UTW RFW 0.003036 0.44743 5.24017
62 5E58 CPZ 0.02377 0.40295 5.27383
63 4Q4K FMN 0.000003662 0.45953 5.32213
64 2C6Q NDP 0.002431 0.40549 5.41311
65 5ABF XRJ 0.02677 0.4017 5.43478
66 2GOU FMN 0.00001584 0.4662 5.47945
67 2VOH CIT 0.01123 0.43068 5.73248
68 2F6U CIT 0.009293 0.44483 5.98291
69 4RJD TFP 0.03977 0.41173 6.06061
70 1ICP FMN 0.000003639 0.4724 6.25
71 1DZK PRZ 0.01236 0.41799 6.36943
72 4YEE 4CQ 0.04094 0.41157 6.66667
73 1UJP CIT 0.01514 0.41044 7.01107
74 3C3N FMN 0.000175 0.43671 7.05128
75 3GAY P6T 0.002662 0.43863 7.12074
76 2GJN FMN 0.000006829 0.52955 7.31707
77 2GJN NIS 0.000009295 0.515 7.31707
78 3ATY FMN 0.000009906 0.4416 7.6087
79 3W9Z FMN 0.00001561 0.41667 7.76398
80 1P4C FMN 0.00000328 0.48244 7.88043
81 4YMZ 13P 0.001011 0.49097 8.36653
82 4CW5 FMN 0.000002084 0.43228 8.96739
83 1KBI PYR 0.0000000536 0.52023 9.23913
84 1KBJ FMN 0.00000004133 0.51894 9.23913
85 1TV5 FMN 0.00002069 0.50532 9.51087
86 4ORM 2V6 0.0003432 0.45284 9.51087
87 4ORM ORO 0.0003432 0.45284 9.51087
88 4ORM FMN 0.0003432 0.45284 9.51087
89 5NBW 8SK 0.007661 0.43581 9.81308
90 1TB3 FMN 0.0000004004 0.50883 9.94318
91 3N9R TD3 0.008001 0.43908 10.0977
92 3BW2 FMN 0.000006849 0.46789 10.3261
93 2RDT 2RD 0.000005062 0.47603 10.5978
94 2RDT FMN 0.00000134 0.47355 10.5978
95 1AL8 FMN 0.0000004599 0.47786 10.8635
96 1AL8 DHP 0.000003626 0.47647 10.8635
97 2NLI FMN 0.00000009544 0.49669 10.8696
98 2NLI LAC 0.01592 0.40802 10.8696
99 4AU8 Z3R 0.03749 0.40424 11.1486
100 4XP7 FNR 0.0000005294 0.45262 11.5607
101 1OVD ORO 0.0001174 0.44543 13.1833
102 1OVD FMN 0.0001174 0.44543 13.1833
103 2B4G FMN 0.000161 0.41317 13.5647
104 3OIX FMN 0.0001097 0.40761 13.6232
105 1EP2 ORO 0.00002173 0.46503 13.7931
106 1EP2 FMN 0.00001909 0.44475 13.7931
107 5EYW PGA 0.003567 0.4621 14.4578
108 3B0P FMN 0.0000006575 0.43897 18
109 5VSM MET 0.01405 0.40581 20.7547
110 5VSM 5AD 0.01809 0.4008 20.7547
111 1F76 FMN 0.000005378 0.4538 22.619
Pocket No.: 4; Query (leader) PDB : 2ZRU; Ligand: FMN; 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: 2zru.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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