Receptor
PDB id Resolution Class Description Source Keywords
4RNX 1.25 Å EC: 1.6.99.1 K154 CIRCULAR PERMUTATION OF OLD YELLOW ENZYME SACCHAROMYCES PASTORIANUS CIRCULAR PERMUTATION CATALYSIS OLD YELLOW ENZYME FLAVIN COXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME ACS CATALYSIS V. 5 892 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:505;
A:503;
A:504;
B:502;
A:502;
B:503;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
FMN B:501;
A:501;
Valid;
Valid;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RNX 1.25 Å EC: 1.6.99.1 K154 CIRCULAR PERMUTATION OF OLD YELLOW ENZYME SACCHAROMYCES PASTORIANUS CIRCULAR PERMUTATION CATALYSIS OLD YELLOW ENZYME FLAVIN COXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME ACS CATALYSIS V. 5 892 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4RNX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4RNX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
12 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
14 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
15 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
18 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
20 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
21 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
22 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
23 2ABB - IPA C3 H8 O CC(C)O
24 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
25 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
26 2GQ9 - HBA C7 H6 O2 c1cc(ccc1C....
27 2GQ8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 2GOU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
29 2GQA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
30 2HS8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
31 2HS6 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
32 3HGO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
33 2HSA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
34 3HGS - PHB C7 H6 O3 c1cc(ccc1C....
35 1OYB - HBA C7 H6 O2 c1cc(ccc1C....
36 1OYC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
37 1BWK - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
38 1OYA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
39 4M5P - MLA C3 H4 O4 C(C(=O)O)C....
40 4TMB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
41 4TMC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
42 1ICS - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
43 3HGR - PHB C7 H6 O3 c1cc(ccc1C....
44 1ICP - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
45 1ICQ - OPD C18 H28 O3 CCC=CC[C@@....
46 3ATY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
47 3ATZ - HBA C7 H6 O2 c1cc(ccc1C....
48 1Q45 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
49 2Q3O - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50 2R14 Kd = 0.63 mM TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
51 3GX9 - TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
52 1GWJ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
53 1VJI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
54 2Q3R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
55 4JIQ Kd = 0.73 mM 1L5 C9 H9 N O2 C/C(=CN(=O....
56 4JIP - HBA C7 H6 O2 c1cc(ccc1C....
57 4JIC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
58 5N6G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
59 4QNW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
60 4RNX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
61 4RNV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
62 4RNW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
63 4A3U - 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RNX; Ligand: FMN; Similar sites found: 98
This union binding pocket(no: 1) in the query (biounit: 4rnx.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TUV VK3 0.01818 0.41893 None
2 1UO4 PIH 0.03277 0.41274 None
3 4TMK T5A 0.03052 0.41243 1.40845
4 4WBD CIT 0.001064 0.47165 1.5
5 1KC7 PPR 0.01659 0.40821 1.5
6 3TFC PEP 0.006989 0.40859 1.55844
7 4AQL TXC 0.001187 0.41006 1.75
8 3ZPG 5GP 0.02605 0.41102 2
9 3MCT 3MC 0.004176 0.41789 2.0202
10 2XI7 XI7 0.02545 0.42655 2.17391
11 3A1I UNU 0.005557 0.40304 2.4952
12 3ICV NAG 0.03638 0.43571 2.53165
13 1JN2 SFP 0.02099 0.41364 2.53165
14 2EB5 OXL 0.01621 0.40315 2.62172
15 3SHR CMP 0.004801 0.40552 2.67559
16 9LDT OXM 0.02511 0.41888 2.71084
17 9LDB OXM 0.03166 0.41354 2.71084
18 1Y1A GSH 0.02098 0.43664 2.73224
19 3ZGE ASP 0.02775 0.40342 2.75
20 3BHO B4P 0.02911 0.41547 2.88462
21 2ZWS PLM 0.001384 0.49624 2.94118
22 1R27 MGD 0.0007268 0.43578 3
23 4RJK PYR 0.02538 0.4053 3
24 3CBG 4FE 0.01279 0.43434 3.01724
25 1HFA PIO 0.001222 0.44042 3.11419
26 1O68 KIV 0.00593 0.41156 3.27273
27 3T2W BTN 0.006009 0.40172 3.27869
28 3TKA CTN 0.002746 0.50308 3.45821
29 3IHB TRS 0.006221 0.49767 3.5
30 2C31 TZD 0.01688 0.40967 3.5
31 2C31 ADP 0.01636 0.40967 3.5
32 4LIT AKG 0.009679 0.40774 3.5
33 3IHB GLU 0.01761 0.40701 3.5
34 2BO4 FLC 0.002647 0.44513 3.52645
35 1P72 THM 0.004919 0.41494 3.59281
36 1C1L GAL BGC 0.01552 0.40956 3.64964
37 2Q3M MLA 0.003842 0.45285 3.68098
38 1V7R CIT 0.01467 0.4312 3.76344
39 3L24 GOA 0.008334 0.43597 3.86847
40 1RYD GLC 0.01792 0.4012 3.87597
41 2NVK NAP 0.002328 0.42844 4
42 4B16 NAG 0.03961 0.40836 4.13534
43 4JCA CIT 0.008275 0.44429 4.19162
44 1ZGA HMK 0.002803 0.40987 4.20168
45 4AF5 CIT 0.01854 0.40054 4.21053
46 3S9K CIT 0.001379 0.50962 4.23729
47 4K30 NLG 0.004439 0.41679 4.25
48 1I2B USQ 0.04231 0.40946 4.25
49 1I2B NAD 0.04231 0.40946 4.25
50 1I2B UPG 0.04231 0.40946 4.25
51 3R51 MMA 0.01924 0.41768 4.375
52 1FIQ MTE 0.003233 0.40479 4.5
53 1GJW GLC 0.02218 0.40234 4.5
54 3LTW HLZ 0.0007594 0.4624 4.64286
55 2CW6 3HG 0.001337 0.4758 4.69799
56 4QVH FLC 0.003417 0.47939 4.75
57 2Q8H TF4 0.009042 0.4342 4.75
58 1XX4 BAM 0.006016 0.41392 4.75
59 4EXO PYR 0.001618 0.46292 4.79452
60 2XUM OGA 0.01079 0.41107 4.87106
61 1HSJ GLC 0.005653 0.46265 5
62 3I7S PYR 0.02085 0.40944 5.13699
63 3P3N AKG 0.01141 0.40998 5.15759
64 3UEC ALA ARG TPO LYS 0.006883 0.42594 5.47945
65 4B9E FAH 0.001617 0.45502 5.64784
66 1YOA FMN 0.01806 0.43481 5.66038
67 2OWZ CIT 0.004746 0.42698 5.72289
68 1H16 PYR 0.007514 0.43085 5.75
69 1H16 DTL 0.0299 0.40799 5.75
70 3UDG TMP 0.01169 0.42859 5.98007
71 1RYI GOA 0.03915 0.4159 6.02094
72 1ZZ7 S0H 0.01083 0.40067 6.06061
73 1F1V DHY 0.006598 0.40472 6.19195
74 4F8L GAL 0.01533 0.43875 6.2069
75 2QLX RM4 0.01107 0.41637 6.48148
76 2OKK ABU 0.009678 0.42556 6.5
77 1GPJ CIT 0.01804 0.40106 6.5
78 3F81 STT 0.03378 0.40529 6.55738
79 2VMD MBG 0.0383 0.40251 6.61479
80 4A6F SEP 0.04247 0.40674 6.66667
81 3QDW NDG 0.002453 0.44666 6.99301
82 3QDW A2G 0.03221 0.40634 6.99301
83 3QDT A2G GAL 0.02493 0.40567 6.99301
84 3IOI 1GW 0.005113 0.40031 7.04698
85 4M51 BEZ 0.009479 0.42599 7.25995
86 1BTN I3P 0.0189 0.42986 7.54717
87 3EW2 BTN 0.005598 0.4076 8.14815
88 2W3L DRO 0.01776 0.41943 9.02778
89 1WTC ACP 0.009391 0.41969 9.25
90 1NU4 MLA 0.009655 0.44077 9.27835
91 3NNF AKG 0.01676 0.4025 10.4651
92 2YD6 FLC 0.005789 0.47207 11.3208
93 1T0S BML 0.0107 0.42346 12.7273
94 1H2M OGA 0.01589 0.40354 13.4615
95 1SS4 GSH 0.004909 0.47416 13.7255
96 1SS4 CIT 0.01041 0.44611 13.7255
97 2OFE NAG 0.01315 0.40722 14.7887
98 2BZ1 TAU 0.01425 0.44051 19.3878
Pocket No.: 2; Query (leader) PDB : 4RNX; Ligand: FMN; Similar sites found: 61
This union binding pocket(no: 2) in the query (biounit: 4rnx.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.0006911 0.51488 None
2 2GWD GLU 0.006712 0.40625 1
3 2H6T IVA VAL VAL STA ALA STA 0.002082 0.40357 1.47059
4 3MAG 3MA 0.007142 0.44946 1.9544
5 2ZJ5 ADP 0.01035 0.40826 2
6 4HA6 PXM 0.004386 0.42441 2.25
7 4OYA 1VE 0.0294 0.40698 2.25
8 2XNJ FAD 0.009617 0.40461 2.25564
9 1PEA ACM 0.006138 0.43692 2.33766
10 3E5P PPI 0.04264 0.43197 2.42588
11 1SQ5 PAU 0.003897 0.42103 2.5974
12 2XDQ MGX 0.04218 0.40199 2.75
13 3MD0 GDP 0.005301 0.41041 2.8169
14 1C3V PDC 0.009063 0.41076 2.85714
15 2WGC SIA GAL BGC 0.04391 0.41493 2.92398
16 4O8A 2OP 0.01027 0.4332 3
17 3CBG FER 0.02037 0.41813 3.01724
18 2JBH 5GP 0.002882 0.42112 3.11111
19 3I6B KDO 0.01072 0.40263 3.33333
20 1YFZ IMP 0.003433 0.42901 3.41463
21 3U1T MLI 0.01118 0.41795 3.55987
22 1JAC AMG 0.03429 0.41334 3.7594
23 2NLI LAC 0.01588 0.40124 3.80435
24 1OGD RIP 0.005769 0.4139 3.81679
25 1H8G CHT 0.00777 0.45685 4.21053
26 3WCS MAN NAG 0.001455 0.43891 4.33071
27 4COQ SAN 0.01529 0.40603 4.45344
28 1FIQ SAL 0.003501 0.40271 4.5
29 1WHT BZS 0.005056 0.42761 4.57516
30 1DXY COI 0.03508 0.40609 4.8048
31 4JP3 CIT 0.004582 0.40368 5.02092
32 4DN8 BMA 0.009264 0.41581 5.12821
33 4B7E OGA 0.009709 0.40946 5.15759
34 1ZJ6 G3D 0.002374 0.41454 5.88235
35 1C7R PA5 0.004074 0.41018 6
36 1RZM E4P 0.01045 0.41932 6.21302
37 1RZM PEP 0.007509 0.40911 6.21302
38 3BY8 MLT 0.004445 0.4366 6.33803
39 2Z9V PXM 0.007139 0.41003 6.63265
40 3QDY A2G GAL 0.02051 0.41149 6.99301
41 3QDY CBS 0.01836 0.40788 6.99301
42 1T3D CYS 0.009843 0.42053 7.61246
43 1NP0 NGT 0.006617 0.42237 7.88382
44 1JGS SAL 0.003375 0.47687 7.97101
45 1Y2W NAG 0.00955 0.41522 8.4507
46 3SQG COM 0.01158 0.43838 8.5
47 2V5E SCR 0.01465 0.43298 8.5
48 3NFZ 3NF 0.004867 0.40268 8.56269
49 4K7O EKZ 0.01395 0.41346 8.92857
50 2QCX PF1 0.006976 0.41569 9.5057
51 2ZYF AKG 0.003115 0.41976 10.5
52 1W3R PYR 0.0174 0.41497 10.6481
53 2VQ5 LDP 0.03487 0.40622 10.9453
54 2VQ5 HBA 0.02624 0.4006 10.9453
55 4LO6 SIA GAL 0.02806 0.40197 13.6842
56 2OFD NGA 0.01067 0.41306 14.7887
57 1Z44 FMN 0.04244 0.40185 15.6805
58 1H2K OGA 0.005644 0.42547 17.0732
59 4F4S EFO 0.01182 0.40084 17.1053
60 1Y7P RIP 0.0103 0.41374 19.7309
61 1O9U ADZ 0.04078 0.40274 27.7778
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