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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 510 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 391 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 298 families.
1 4YBN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 FAD 1 1
2 FAS 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 FAE 0.751773 0.987654
7 SFD 0.651007 0.860215
8 FDA 0.641892 0.906977
9 FNK 0.602564 0.876405
10 62F 0.572327 0.939024
11 F2N 0.566265 0.886364
12 FMN 0.543307 0.876543
13 FA9 0.526316 0.939759
14 6YU 0.516304 0.860215
15 P6G FDA 0.511628 0.908046
16 FAD NBT 0.508876 0.83871
17 A2D 0.504065 0.875
18 P5F 0.491329 0.941176
19 FAD CNX 0.488506 0.8125
20 AR6 0.488372 0.851852
21 APR 0.488372 0.851852
22 AGS 0.484615 0.811765
23 SAP 0.484615 0.811765
24 M33 0.484375 0.864198
25 BA3 0.484127 0.875
26 HEJ 0.48062 0.851852
27 ATP 0.48062 0.851852
28 ADP 0.480315 0.851852
29 B4P 0.480315 0.875
30 AP5 0.480315 0.875
31 ANP 0.477273 0.831325
32 AQP 0.476923 0.851852
33 5FA 0.476923 0.851852
34 48N 0.469388 0.902439
35 OAD 0.467626 0.876543
36 9X8 0.467626 0.833333
37 FAD NBA 0.467033 0.793814
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AT4 0.465116 0.821429
41 AD9 0.462121 0.831325
42 3OD 0.460993 0.876543
43 RBF 0.460938 0.790123
44 FB0 0.460606 0.835165
45 139 0.460526 0.858824
46 AP0 0.46 0.835294
47 A22 0.459854 0.864198
48 ACP 0.458015 0.853659
49 8QN 0.456522 0.864198
50 PRX 0.454545 0.831325
51 A3R 0.453237 0.86747
52 A1R 0.453237 0.86747
53 G3A 0.452055 0.902439
54 T5A 0.45098 0.872093
55 G5P 0.44898 0.902439
56 ATF 0.448529 0.821429
57 50T 0.44697 0.819277
58 6YZ 0.445255 0.853659
59 ACQ 0.444444 0.853659
60 CNV FAD 0.443182 0.917647
61 ADQ 0.442857 0.853659
62 PAJ 0.442857 0.847059
63 5AL 0.441176 0.864198
64 ADX 0.439394 0.775281
65 CA0 0.439394 0.853659
66 A4P 0.437909 0.831461
67 25L 0.4375 0.864198
68 P33 FDA 0.436464 0.817204
69 5SV 0.435714 0.793103
70 OMR 0.434211 0.818182
71 TXE 0.434211 0.890244
72 ABM 0.434109 0.829268
73 A 0.433071 0.82716
74 AMP 0.433071 0.82716
75 4AD 0.432624 0.855422
76 ADJ 0.432258 0.818182
77 B5M 0.431507 0.878049
78 B5Y 0.431507 0.878049
79 BIS 0.430556 0.802326
80 SRA 0.429688 0.788235
81 AFH 0.42953 0.825581
82 NXX 0.427632 0.865854
83 DND 0.427632 0.865854
84 UP5 0.427632 0.878049
85 6V0 0.427632 0.857143
86 TXD 0.427632 0.890244
87 DQV 0.426667 0.8875
88 SRP 0.42446 0.843373
89 PR8 0.423611 0.837209
90 T99 0.423358 0.821429
91 TAT 0.423358 0.821429
92 AMO 0.422535 0.865854
93 TXA 0.42069 0.865854
94 FYA 0.42069 0.864198
95 PTJ 0.42069 0.835294
96 CNA 0.420382 0.865854
97 00A 0.41958 0.823529
98 AHX 0.41958 0.835294
99 MAP 0.41844 0.811765
100 NAI 0.418301 0.845238
101 AU1 0.41791 0.831325
102 A12 0.416667 0.843373
103 AP2 0.416667 0.843373
104 25A 0.415493 0.851852
105 9ZA 0.415493 0.845238
106 9ZD 0.415493 0.845238
107 COD 0.415094 0.842697
108 4TC 0.412903 0.879518
109 APC 0.411765 0.843373
110 ME8 0.410959 0.806818
111 1ZZ 0.410959 0.806818
112 NB8 0.410959 0.835294
113 4UW 0.409091 0.825581
114 NAX 0.409091 0.837209
115 F2R 0.408805 0.850575
116 RBY 0.408759 0.843373
117 ADV 0.408759 0.843373
118 P1H 0.405882 0.818182
119 OOB 0.405594 0.864198
120 LAD 0.40411 0.825581
121 A A 0.40411 0.829268
122 UPA 0.403846 0.86747
123 4UU 0.401316 0.833333
124 GA7 0.401316 0.865854
125 A3D 0.401235 0.876543
126 80F 0.401235 0.808989
127 XAH 0.4 0.806818
128 DLL 0.4 0.864198
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YBN; Ligand: FAD; Similar sites found with APoc: 197
This union binding pocket(no: 1) in the query (biounit: 4ybn.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4K55 H6P None
2 2BVE PH5 None
3 3R5W F42 None
4 1KZL CRM None
5 3TW1 AHN 0.892857
6 4EE7 PIS 1.78571
7 3B6R ADP 1.78571
8 3KYF 5GP 5GP 1.78571
9 2AXR ABL 1.78571
10 4HWS 1B3 1.78571
11 4KBA 1QM 1.81269
12 5W4W 9WG 1.81269
13 2GJ5 VD3 1.85185
14 5AYT L6Y 1.88679
15 2P39 SCR 1.93548
16 1QKQ MAN 2.11268
17 1SDW IYT 2.23214
18 5D9G GLU ASN LEU TYR PHE GLN 2.23214
19 2RDE C2E 2.23214
20 4UWJ MYA 2.23214
21 4UWJ 7L5 2.23214
22 5C3R HMU 2.23214
23 5C3R AKG 2.23214
24 4U0W 16G 2.23214
25 4YVN EBS 2.23214
26 1OUK 084 2.23214
27 5TUF TDC 2.23214
28 2JC9 ADN 2.23214
29 5KY9 GDP 2.23214
30 3GD8 GOL 2.24215
31 3TCT 3MI 2.3622
32 1KGI T4A 2.3622
33 1F5F DHT 2.43902
34 5OCG 9R5 2.6455
35 2O1C PPV 2.66667
36 2PNC CLU 2.67857
37 3JU6 ANP 2.67857
38 5C5T AKG 2.67857
39 5T96 79J 2.67857
40 3FXU TSU 2.67857
41 6EWZ APC 2.67857
42 4RF7 ARG 2.67857
43 1ODM ASV 2.67857
44 6GWR FEW 2.67857
45 4XZ3 ACP 2.67857
46 2WEL K88 2.75229
47 2GTF P1R 2.77778
48 6FA4 D1W 2.89017
49 2ASF CIT 2.91971
50 6GNO XDI 2.96296
51 3TAY MN0 3.06748
52 4MOB ADP 3.125
53 5KJW 53C 3.125
54 3GD9 GLC BGC BGC BGC 3.125
55 3W9F I3P 3.125
56 2WSA MYA 3.125
57 2WSA 646 3.125
58 1I1E DM2 3.125
59 5HWV MBN 3.125
60 4WOE ADP 3.125
61 3G1Z AMP 3.125
62 4ZTD ALA GLY ALA GLY ALA 3.125
63 5H9Y BGC BGC BGC BGC 3.125
64 4BTV RB3 3.125
65 5LGA 6VH 3.125
66 1C3X 8IG 3.125
67 6MPT C30 3.125
68 3QRC SCR 3.18471
69 5F6U 5VK 3.18471
70 3UEC ALA ARG TPO LYS 3.42466
71 1F9V ADP 3.57143
72 3JQ3 ADP 3.57143
73 5M90 JIF 3.57143
74 4HMT FMN 3.57143
75 4HMT NNV 3.57143
76 5YJS SAL 3.57143
77 4YRI 4JH 3.57143
78 5J75 6GQ 3.57143
79 4C2C ALA ALA ALA 3.57143
80 3QPB URA 3.57143
81 1RJW ETF 3.57143
82 4U60 SIA GAL NGA 3.57143
83 5LUN OGA 3.57143
84 4U60 SIA 3.57143
85 3DLG GWE 3.57143
86 1M15 ARG 3.57143
87 1M15 ADP 3.57143
88 5MU6 MYA 3.58056
89 5MU6 KFK 3.58056
90 1T9M FMN 3.73832
91 5OUH L0B 3.90244
92 5DYO FLU 4.01786
93 4CS4 AXZ 4.01786
94 2NZ2 CIR 4.01786
95 4CS4 ANP 4.01786
96 1UNB PN1 4.01786
97 1UNB AKG 4.01786
98 3ACL 3F1 4.01786
99 5EQ8 HSO 4.01786
100 5MRH Q9Z 4.01786
101 4W9N TCL 4.01786
102 1U6R ADP 4.01786
103 5XEG AKG 4.01786
104 6CC0 EWM 4.01786
105 3CBC DBS 4.0404
106 3L5R 47X 4.09836
107 3HCH RSM 4.10959
108 4HMX WUB 4.18605
109 4HMX FMN 4.18605
110 3E85 BSU 4.43038
111 1VRP ADP 4.46429
112 1RYD GLC 4.46429
113 5ZIC BMA Z4Y NAG 4.46429
114 1ZDQ MSM 4.46429
115 4WHZ 3NL 4.46429
116 3T4L ZEA 4.46429
117 4C3Y FAD 4.46429
118 2EPN NGT 4.46429
119 2QTZ FAD 4.46429
120 1P0Z FLC 4.58015
121 3R5Y F42 4.7619
122 2G30 ALA ALA PHE 4.91071
123 4P8K 38C 4.91071
124 4P8K FAD 4.91071
125 1HXD BTN 4.91071
126 4XIZ LPP 5.29412
127 5FUI APY 5.30303
128 4JX1 CAH 5.30973
129 5G48 1FL 5.35714
130 5H2U 1N1 5.35714
131 1U18 HSM 5.40541
132 4IEN GDP 5.52147
133 2AGC DAO 5.55556
134 1QY1 PRZ 5.74713
135 2VDF OCT 5.80357
136 2YKL NLD 5.80357
137 5HV7 RBL 5.80357
138 5LXT GTP 5.80357
139 6C1S EFV 5.80357
140 4ZSI GLP 5.84795
141 5TZO 7V7 5.85106
142 4WO4 JLS 6
143 5WL1 CUY 6.06061
144 5WL1 D3D 6.06061
145 1OFL NGK GCD 6.25
146 6C5F 7L9 6.25
147 1G79 FMN 6.42202
148 1G79 PLP 6.42202
149 5IXG OTP 6.50888
150 4BG4 ADP 6.69643
151 1NE7 16G 6.69643
152 4DE3 DN8 6.69643
153 5A89 FMN 6.69643
154 5A89 ADP 6.69643
155 4FK7 P34 6.69643
156 3G5D 1N1 6.69643
157 3G08 FEE 7.07071
158 3RUG DB6 7.07071
159 5X7Q GLC GLC GLC GLC 7.14286
160 3A3B FMN 7.36842
161 1U0A BGC BGC BGC BGC 7.47664
162 5H9P TD2 7.59494
163 4RYV ZEA 7.74194
164 4IAW LIZ 7.97872
165 3TTZ 07N 8.08081
166 4RD0 GDP 8.48214
167 2Q8E OGA 8.48214
168 2YBP 2HG 8.48214
169 5MJA 7O3 8.48214
170 1EP2 FAD 8.48214
171 4OYA 1VE 8.92857
172 3H0L ADP 8.92857
173 2Z3U CRR 9.375
174 4TW7 37K 9.375
175 4JCA CIT 9.58084
176 1OPB RET 9.70149
177 5KR7 6X9 10.2679
178 3R5Z F42 10.3448
179 1S5O 152 10.7143
180 4F7E 0SH 11.1607
181 3L9R L9R 11.1607
182 4QVB F42 11.5646
183 3NZ1 3NY 12.0536
184 4OFJ HIS 12.5
185 6E1Q CFA 12.5
186 3VRV YSD 12.5
187 2AG4 OLA 12.8049
188 2AG4 LP3 12.8049
189 2Z77 HE7 12.9496
190 5O0X FAD 13.3929
191 3MF2 AMP 13.3929
192 1I7M PUT 14.9254
193 4YRY FAD 15.625
194 1BC5 ACE ASN TRP GLU THR PHE 16.0714
195 1GT4 UNA 18.239
196 1PVC ILE SER GLU VAL 20.0893
197 5CLO NS8 20.339
Pocket No.: 2; Query (leader) PDB : 4YBN; Ligand: FAD; Similar sites found with APoc: 74
This union binding pocket(no: 2) in the query (biounit: 4ybn.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 4CS9 AMP None
2 1ZEI CRS None
3 3OQJ 3CX 0.892857
4 4XMF HSM 1.08696
5 6AZQ C5J 1.14504
6 4M6T SAM 2.18579
7 5KXQ GDP 2.23214
8 5KY5 GDP 2.23214
9 2JBM SRT 2.23214
10 5KY4 GDP 2.23214
11 5Z54 0HZ 2.23214
12 1EQ2 ADQ 2.58065
13 2F7C CCU 2.67857
14 3CL5 SIO 2.67857
15 1IYB 5GP 2.67857
16 6A46 DCM 2.67857
17 5YRL GLC GLC 2.8169
18 4RJD TFP 3.0303
19 2WW2 SWA 3.125
20 4WCX MET 3.125
21 5UXH GFB 3.125
22 1YFS ALA 3.125
23 3ZJX BOG 3.125
24 3KDM TES 3.21101
25 4M44 SIA GAL NAG GAL 3.2967
26 1JAY F42 3.30189
27 2Z9V PXM 3.57143
28 5KL0 G16 3.57143
29 2YIP YIO 3.62319
30 1CT9 AMP 4.01786
31 5N6N SUC 4.01786
32 2X0K PPV 4.01786
33 1LCF OXL 4.01786
34 2ZX2 RAM 4.10256
35 3W6G FLC 4.16667
36 2ZWI C5P 4.28954
37 3IIJ ADP 4.44444
38 2QHV OC9 4.46429
39 2QHS OCA 4.46429
40 1GPM AMP 4.46429
41 5FPE 3TR 4.46429
42 6FXR AKG 4.46429
43 4K7O EKZ 4.7619
44 3P13 RIP 4.86111
45 5N0O SAM 4.91071
46 5YRV 5AD 4.91071
47 4G6I RS3 5.2381
48 2V2G BEZ 5.35714
49 2CYC TYR 5.35714
50 2VQ5 HBA 5.47264
51 3KJQ B94 5.4878
52 4FE2 AIR 5.4902
53 2WVZ KIF 5.80357
54 3A51 VDY 5.80357
55 4KVL PLM 6.25
56 4DDY DN6 6.69643
57 4FFG 0U8 7.14286
58 5X7Q GLC GLC GLC GLC GLC 7.14286
59 3A3B RBF 7.36842
60 1T36 ORN 7.58929
61 5CPR 539 8.48214
62 5OES ADP 8.92857
63 5EY0 ILE 8.92857
64 1PNF NDG NAG 8.92857
65 3FSY SCA 9.375
66 2W9S TOP 9.93789
67 5O9W AKG 11.1607
68 6CED EYA 11.215
69 5YRG BGC GLC 11.2676
70 6MJF SAH 13.3929
71 3DZ6 PUT 14.9254
72 4J4V SVR 16.9643
73 1F76 ORO 16.9643
74 5C2N NAG 25
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