Receptor
PDB id Resolution Class Description Source Keywords
4YBN 1.9 Å NON-ENZYME: BINDING STRUCTURE OF THE FAD AND HEME BINDING PROTEIN MSMEG_4975 FRO MYCOBACTERIUM SMEGMATIS MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 7MC(2)155) OXIDOREDUCTASE FAD HEME SPLIT BETA-BARREL
Ref.: SEQUENCE-STRUCTURE-FUNCTION CLASSIFICATION OF A CATALYTICALLY DIVERSE OXIDOREDUCTASE SUPERFAMILY IN MYCOBACTERIA. J.MOL.BIOL. V. 427 3554 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM A:304;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
SO4 B:304;
A:302;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
NI A:301;
B:303;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
FAD B:305;
B:302;
Valid;
Valid;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
ACT A:303;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YBN 1.9 Å NON-ENZYME: BINDING STRUCTURE OF THE FAD AND HEME BINDING PROTEIN MSMEG_4975 FRO MYCOBACTERIUM SMEGMATIS MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 7MC(2)155) OXIDOREDUCTASE FAD HEME SPLIT BETA-BARREL
Ref.: SEQUENCE-STRUCTURE-FUNCTION CLASSIFICATION OF A CATALYTICALLY DIVERSE OXIDOREDUCTASE SUPERFAMILY IN MYCOBACTERIA. J.MOL.BIOL. V. 427 3554 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 4YBN - FAD C27 H33 N9 O15 P2 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 355 families.
1 4YBN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 4YBN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 DAL FAD PER 0.772414 0.951807
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 62F 0.572327 0.939024
12 F2N 0.566265 0.886364
13 FMN 0.543307 0.876543
14 FA9 0.526316 0.939759
15 6YU 0.516304 0.860215
16 CNV FAD 0.511905 0.908046
17 P6G FDA 0.511628 0.908046
18 FAD NBT 0.508876 0.83871
19 A2D 0.504065 0.875
20 P5F 0.491329 0.941176
21 FAD CNX 0.488506 0.8125
22 APR 0.488372 0.851852
23 AR6 0.488372 0.851852
24 AGS 0.484615 0.811765
25 SAP 0.484615 0.811765
26 M33 0.484375 0.864198
27 BA3 0.484127 0.875
28 FAD NBA 0.480663 0.802083
29 ATP 0.48062 0.851852
30 B4P 0.480315 0.875
31 ADP 0.480315 0.851852
32 AP5 0.480315 0.875
33 ANP 0.477273 0.831325
34 AQP 0.476923 0.851852
35 5FA 0.476923 0.851852
36 48N 0.469388 0.902439
37 OAD 0.467626 0.876543
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AD9 0.462121 0.831325
41 3OD 0.460993 0.876543
42 RBF 0.460938 0.790123
43 FB0 0.460606 0.835165
44 139 0.460526 0.858824
45 AP0 0.46 0.835294
46 A22 0.459854 0.864198
47 ACP 0.458015 0.853659
48 8QN 0.456522 0.864198
49 PRX 0.454545 0.831325
50 A1R 0.453237 0.86747
51 G3A 0.452055 0.902439
52 T5A 0.45098 0.872093
53 G5P 0.44898 0.902439
54 ATF 0.448529 0.821429
55 50T 0.44697 0.819277
56 ACQ 0.444444 0.853659
57 PAJ 0.442857 0.847059
58 ADQ 0.442857 0.853659
59 5AL 0.441176 0.864198
60 ADX 0.439394 0.775281
61 CA0 0.439394 0.853659
62 A4P 0.437909 0.831461
63 25L 0.4375 0.864198
64 P33 FDA 0.436464 0.817204
65 5SV 0.435714 0.793103
66 TXE 0.434211 0.890244
67 OMR 0.434211 0.818182
68 ABM 0.434109 0.829268
69 A 0.433071 0.82716
70 AMP 0.433071 0.82716
71 4AD 0.432624 0.855422
72 ADJ 0.432258 0.818182
73 BIS 0.430556 0.802326
74 SRA 0.429688 0.788235
75 AFH 0.42953 0.825581
76 TXD 0.427632 0.890244
77 NXX 0.427632 0.865854
78 UP5 0.427632 0.878049
79 DND 0.427632 0.865854
80 6V0 0.427632 0.857143
81 SRP 0.42446 0.843373
82 PR8 0.423611 0.837209
83 TAT 0.423358 0.821429
84 AMO 0.422535 0.865854
85 PTJ 0.42069 0.835294
86 FYA 0.42069 0.864198
87 TXA 0.42069 0.865854
88 CNA 0.420382 0.865854
89 00A 0.41958 0.823529
90 AHX 0.41958 0.835294
91 MAP 0.41844 0.811765
92 NAI 0.418301 0.845238
93 AU1 0.41791 0.831325
94 AP2 0.416667 0.843373
95 A12 0.416667 0.843373
96 25A 0.415493 0.851852
97 AMP MG 0.415385 0.785714
98 COD 0.415094 0.842697
99 ADP BEF 0.414815 0.77907
100 BEF ADP 0.414815 0.77907
101 4TC 0.412903 0.879518
102 APC 0.411765 0.843373
103 NB8 0.410959 0.835294
104 ME8 0.410959 0.806818
105 1ZZ 0.410959 0.806818
106 4UW 0.409091 0.825581
107 NAX 0.409091 0.837209
108 RBY 0.408759 0.843373
109 ADV 0.408759 0.843373
110 ADP MG 0.407407 0.797619
111 P1H 0.405882 0.818182
112 OOB 0.405594 0.864198
113 A A 0.40411 0.829268
114 LAD 0.40411 0.825581
115 UPA 0.403846 0.86747
116 4UU 0.401316 0.833333
117 A3D 0.401235 0.876543
118 DLL 0.4 0.864198
119 XAH 0.4 0.806818
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YBN; Ligand: FAD; 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: 4ybn.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4YBN; Ligand: FAD; Similar sites found: 35
This union binding pocket(no: 2) in the query (biounit: 4ybn.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3R5W F42 0.004588 0.42273 None
2 4XMF HSM 0.006463 0.43798 1.08696
3 4KBA 1QM 0.01139 0.42729 1.81269
4 4YVN EBS 0.0208 0.4192 2.23214
5 2JBM SRT 0.01525 0.4175 2.23214
6 5KY5 GDP 0.01976 0.40714 2.23214
7 4RJD TFP 0.03699 0.40316 3.0303
8 1I1E DM2 0.02385 0.41478 3.125
9 4WCX MET 0.0349 0.40936 3.125
10 5UXH GFB 0.008204 0.40812 3.125
11 3ZJX BOG 0.04114 0.40492 3.125
12 3JQ3 ADP 0.0006873 0.48436 3.57143
13 4HMT NNV 0.0009335 0.41646 3.57143
14 4HMT FMN 0.000766 0.41646 3.57143
15 4U60 SIA GAL NGA 0.02647 0.40948 3.57143
16 4U60 SIA 0.0303 0.4057 3.57143
17 1T9M FMN 0.0001522 0.4943 3.73832
18 5MRH Q9Z 0.009344 0.43174 4.01786
19 4W9N TCL 0.02951 0.40984 4.01786
20 3W6G FLC 0.02123 0.41749 4.16667
21 2QHV OC9 0.004538 0.44794 4.46429
22 2QHS OCA 0.006993 0.43369 4.46429
23 3P13 RIP 0.008125 0.45841 4.86111
24 2G30 ALA ALA PHE 0.0003222 0.47433 4.91071
25 2CYC TYR 0.03962 0.40553 5.35714
26 4FE2 AIR 0.01438 0.41788 5.4902
27 2VDF OCT 0.007317 0.41802 5.80357
28 4BG4 ADP 0.006814 0.41844 6.69643
29 4FFG 0U8 0.02432 0.41434 7.14286
30 4IAW LIZ 0.01308 0.41996 7.97872
31 1OPB RET 0.00313 0.43021 9.70149
32 2AG4 LP3 0.007676 0.41331 12.8049
33 2AG4 OLA 0.006813 0.41331 12.8049
34 1I7M PUT 0.02736 0.40275 14.9254
35 1GT4 UNA 0.01326 0.40845 18.239
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