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Receptor
PDB id Resolution Class Description Source Keywords
5Y6Q 2.5 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF AN ALDEHYDE OXIDASE FROM METHYLOBACILLU KY4400 METHYLOBACILLUS SP. KY4400 ALDEHYDE OXIDASE MOLYBDENUM ENZYME METHYLOBACILLUS SP. KY440OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF AN ALDEHYDE OXIDASE FROM METHYLOBACILLUS SP. KY4400. J. BIOCHEM. V. 163 321 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IPA C:815;
C:816;
Invalid;
Invalid;
none;
none;
submit data
60.095 C3 H8 O CC(C)...
SF4 B:402;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
9421_9422_9423_9424_ C:801;
Invalid;
none;
submit data n/a n/a n/a n/a
SO4 C:806;
C:803;
C:807;
A:203;
B:403;
C:805;
B:404;
C:808;
B:405;
C:810;
C:809;
C:804;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
FES A:201;
A:202;
Part of Protein;
Part of Protein;
none;
none;
submit data
175.82 Fe2 S2 S1[Fe...
GOL B:406;
C:812;
C:811;
C:813;
B:407;
C:814;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
FAD B:401;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
MCN C:802;
Valid;
none;
submit data
696.501 C19 H22 N8 O13 P2 S2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5Y6Q 2.5 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF AN ALDEHYDE OXIDASE FROM METHYLOBACILLU KY4400 METHYLOBACILLUS SP. KY4400 ALDEHYDE OXIDASE MOLYBDENUM ENZYME METHYLOBACILLUS SP. KY440OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF AN ALDEHYDE OXIDASE FROM METHYLOBACILLUS SP. KY4400. J. BIOCHEM. V. 163 321 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 5Y6Q - 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 280 families.
1 5Y6Q - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5G5H - MCN C19 H22 N8 O13 P2 S2 C1=CN(C(=O....
2 5G5G - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 5Y6Q - 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
Ligand no: 2; Ligand: MCN; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 MCN 1 1
2 CDP 0.557692 0.819277
3 HF4 0.542056 0.819277
4 CTP 0.542056 0.819277
5 C2G 0.535714 0.809524
6 CDC 0.517241 0.712766
7 CDM 0.512821 0.764045
8 7XL 0.508929 0.8
9 C5G 0.508475 0.821429
10 PCD 0.496403 0.909091
11 CXY 0.491667 0.821429
12 C5P 0.485714 0.807229
13 CAR 0.485714 0.807229
14 C 0.485714 0.807229
15 1AA 0.484127 0.857143
16 C C C C 0.442623 0.797619
17 C C 0.441667 0.807229
18 2AA 0.438849 0.737864
19 CSQ 0.426357 0.833333
20 CSV 0.426357 0.833333
21 91P 0.414286 0.873563
22 CTN 0.403846 0.722892
23 AR3 0.403846 0.722892
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5Y6Q; Ligand: FAD; Similar sites found with APoc: 196
This union binding pocket(no: 1) in the query (biounit: 5y6q.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 2MBR FAD 2.72727
2 2MBR EPU 2.72727
3 4TQK NAG 2.72727
4 1G41 ADP 3.08642
5 4MGB XDH 3.13725
6 2BJ4 OHT 3.1746
7 2Q4W FAD 3.24427
8 4G6I RS3 3.33333
9 1U1W 3HA 3.3557
10 6HKE LMR 3.45912
11 1MZV AMP 3.7037
12 1OHE ACE ALA SEP PRO 3.7037
13 3A70 NPO 3.7037
14 4AVV CD 3.92157
15 4WCX ALA 3.93939
16 3OZG SSI 4
17 4JZ8 CIT 4.10095
18 1FDJ 13P 4.13223
19 4L50 D8X 4.13534
20 1QB7 ADE 4.23729
21 3B6C SDN 4.2735
22 1GPJ CIT 4.32099
23 2JKY 5GP 4.69484
24 3QDX CBS 4.8951
25 3QDV NDG 4.8951
26 3QDY CBS 4.8951
27 3QDW NDG 4.8951
28 2UUU FAD 4.93827
29 2UUU PL3 4.93827
30 1GVF PGH 4.93827
31 4B2D FBP 4.93827
32 2X1L MET 4.96183
33 2X1L ADN 4.96183
34 1EKX PAL 5.14469
35 5AE2 FYC 5.15152
36 5AE2 FAD 5.15152
37 1AXW UMP 5.28302
38 1U3G ADP 5.29101
39 2V7B BEZ 5.29301
40 1ZPR UMP 5.30303
41 4FE2 ADP 5.4902
42 6ACS CIT 5.55556
43 4RHY 3QG 5.55556
44 4EWN 0VR 5.55556
45 1DJN ADP 5.55556
46 1D1Q 4NP 5.59006
47 2NZ5 226 5.75758
48 3KL3 GCU 5.75758
49 2OO0 PLP 5.75758
50 1CZA G6P 5.80645
51 1UA4 GLC 5.93407
52 1UA4 BGC 5.93407
53 1G8S MET 6.08696
54 1UJ5 5RP 6.1674
55 5MB4 NDG 6.17284
56 5MB4 NAG 6.17284
57 2HIM ASN 6.17284
58 4PYA 2X3 6.36364
59 1HSK FAD 6.44172
60 2G50 ALA 6.60377
61 4WOH 4NP 6.62651
62 3B6O TMP 6.79012
63 5MBC FMN 6.79012
64 3ITJ CIT 6.80473
65 1U6R ADP 6.84211
66 3IP8 B85 6.85484
67 5HGZ MLA 6.99588
68 2OFE NAG 7.04225
69 2JBH 5GP 7.11111
70 6EK3 OUL 7.23982
71 1PZM 5GP 7.40741
72 1P19 IMP 7.40741
73 3UN3 G16 7.40741
74 1QK3 5GP 7.40741
75 3TDC 0EU 7.40741
76 3S6X SIA GAL BGC 7.40741
77 2UW1 GVM 7.40741
78 4YJI TYL 7.40741
79 5EY0 GTP 7.40741
80 2WZF UDP 7.40741
81 4XDA RIB 7.44337
82 2GQT FAD 7.46269
83 3F81 STT 7.65027
84 4P83 U5P 7.69231
85 4UP4 NDG 7.73067
86 4UP4 NAG 7.73067
87 4UP4 GAL NAG 7.73067
88 5F5R ANP 7.98319
89 3RK0 AMP 8.01688
90 3RK1 ATP 8.01688
91 3ORQ ADP 8.02469
92 5C9P FUC 8.02469
93 5H3A D16 8.02469
94 5BRP PNG 8.09859
95 6G5Q EMZ 8.18182
96 4DOO DAO 8.29268
97 1XTT U5P 8.33333
98 1G27 BB1 8.33333
99 4JLS 3ZE 8.55263
100 5VJN ADE 8.55615
101 5VJN IR8 8.55615
102 3MBI HSX 8.64198
103 2JK0 ASP 8.64198
104 4JB1 NAP 8.64198
105 4JB1 FAD 8.64198
106 2XT3 ADP 8.64198
107 6CBO DOW 8.64198
108 1TRD PGH 8.8
109 2WOR 2AN 9
110 2PS1 ORO 9.25926
111 2PS1 PRP 9.25926
112 2X5D PLP 9.25926
113 5DNC ASN 9.25926
114 4ARE FLC 9.25926
115 3Q2H QHF 9.25926
116 2QS8 MET 9.33014
117 4DE3 DN8 9.39394
118 2AWN ADP 9.39394
119 3L6C MLI 9.39394
120 1D3V ABH 9.39394
121 3F4F UMP 9.58084
122 5YV5 ADP 9.69697
123 1YQT ADP 9.69697
124 1JQY A32 9.70874
125 1F0X FAD 9.87654
126 5LV1 78T 9.87654
127 3C7F XYP XYP XYP 9.87654
128 3BJE R1P 9.87654
129 1DQN IMU 10
130 2I0K FAD 10
131 5E5U MLI 10.0503
132 3V2U GLA 10.274
133 4PC3 GDP 10.4938
134 3W8X FTK 10.4938
135 3W8X FAD 10.4938
136 1UPF URF 10.7143
137 2DT9 THR 10.7784
138 3P48 DUP 10.8844
139 4B4U NAP 10.9091
140 1NVM OXL 11.1111
141 1LYX PGA 11.1111
142 3TAO PGH 11.1111
143 1TLG GAL 11.2
144 2ZSC BTN 11.3475
145 1VBO MAN 11.4094
146 3ACC 5GP 11.7284
147 6BVJ EAS 11.7284
148 3ZFD ANP 11.7284
149 6BVI EC4 11.7284
150 4URX HXY 11.7284
151 4YMZ 13P 11.7284
152 4K91 SIN 11.7284
153 4GV8 DUP 11.7284
154 1HGX 5GP 12.0219
155 4CCW VKC 12.0401
156 4YEE 4CQ 12.2222
157 5CX6 CDP 12.4242
158 5JVB 2PO 12.4242
159 4P86 5GP 12.963
160 5D85 FLC 13.5802
161 4YMU ATP 13.5802
162 5OFW 9TW 13.5802
163 5N53 8NB 13.5802
164 1KZL CRM 13.5802
165 4XFM THE 13.5802
166 4GDX GLU 13.5802
167 1BCJ NGA 13.6364
168 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 13.8075
169 1L1Q 9DA 13.9785
170 2OL1 UMP 14.2857
171 4PPF FLC 14.2857
172 2D2F ADP 14.8148
173 1Q5H DUD 15.6463
174 4JEJ 1GP 16.0606
175 2V57 PRL 16.6667
176 1O5O U5P 16.7421
177 5NBW 8SK 17.1171
178 4JD0 1KH 17.284
179 5HV7 RBL 17.284
180 1X0P FAD 17.4825
181 1WK8 VMS 17.9012
182 3B96 MYA 17.9012
183 4OOP DUP 18.0723
184 1CX4 CMP 18.5185
185 1PVC ILE SER GLU VAL 19.1176
186 4JN6 OXL 19.7531
187 1F7K UMP 20.5882
188 3EYY MLI 20.6897
189 6AR9 3L4 21.3235
190 1LNX URI 23.4568
191 3AB4 THR 27.7778
192 1FIQ FAD 45.0617
193 1V97 FAD 45.0617
194 3NRZ FAD 48.1481
195 4YSW NAI 48.1481
196 4YSW FAD 48.1481
Pocket No.: 2; Query (leader) PDB : 5Y6Q; Ligand: MCN; Similar sites found with APoc: 179
This union binding pocket(no: 2) in the query (biounit: 5y6q.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 5I7Y 69G 2.9703
3 1IXI 2HP 3.08642
4 2VAR AMP 3.19489
5 4G6I RS3 3.33333
6 2J0B UDP 3.57143
7 2Y65 ADP 3.63636
8 3DSK T25 3.63636
9 4XJ7 ADN 3.74532
10 5Y5Q DUT 4.02299
11 1LDN FBP 4.11392
12 3MTW M3R 4.24242
13 5TZO 7V7 4.25532
14 1EB1 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 4.28016
15 2NZ2 ASP 4.32099
16 6AC9 ANP 4.32099
17 1HV9 UD1 4.32099
18 1IIM TTP 4.32099
19 2OFW ADX 4.32692
20 5DEQ ARA 4.38596
21 3LL5 IP8 4.41767
22 1GOJ ADP 4.50704
23 1LVG ADP 4.54545
24 1SQS TLA 4.54545
25 2IOY RIP 4.59364
26 5LQ8 GB 4.60993
27 5ZI9 FLC 4.61538
28 1DCP HBI 4.80769
29 3QDT A2G GAL 4.8951
30 2FJK 13P 4.91803
31 2AK3 AMP 4.93827
32 1GVF PGH 4.93827
33 6AM8 TRP 4.93827
34 6AM8 PLT 4.93827
35 4XFR CIT 4.93827
36 5A7Y SAH 4.93827
37 4XG0 CIT 4.93827
38 4AMV F6R 5.15152
39 1Z0N BCD 5.20833
40 1FWY UD1 5.43807
41 4AG5 ADP 5.45455
42 6GNF GLC 5.55556
43 4CJN QNZ 5.55556
44 5L2R MLA 5.55556
45 1G6H ADP 5.83658
46 3C8E GSH 5.90278
47 3TW1 AHN 5.90717
48 1Y63 ADP 5.97826
49 2AIQ BEN 6.06061
50 1FUR MLT 6.17284
51 1JJV ATP 6.17284
52 4PQG NAG 6.17284
53 3KIH GDL 6.18557
54 1CBK ROI 6.25
55 5UI2 SUC 6.30915
56 6F5W KG1 6.50407
57 5F1H 5U6 6.50407
58 5LPG 71V 6.70732
59 3SBZ MLI 6.74603
60 4FRZ ADP 6.79012
61 1OBD AMP 6.79012
62 3CQL NAG 6.79012
63 2D3Y DU 6.79012
64 5KBF CMP 6.79012
65 4LZB URA 6.79012
66 6GH9 MIX 6.79012
67 3VGL BGC 6.85358
68 4EKQ NPO 6.95187
69 3SHR CMP 7.02341
70 4WQQ MAN 7.0922
71 5TDF ADE 7.40741
72 5FUS DAO 7.40741
73 5ME4 HP4 7.40741
74 4N14 WR7 7.40741
75 3A2Y TS5 7.61421
76 4P83 U5P 7.69231
77 4COQ SAN 7.69231
78 1V2G OCA 7.89474
79 2QPU QPS 7.90123
80 2QPU QPU 7.90123
81 1EU1 GLC 8.02469
82 5JBX MLI 8.02469
83 6GG9 FMN 8.02469
84 5C9P FUC 8.02469
85 3C1M ANP 8.03383
86 3T03 3T0 8.09859
87 6EV2 BGC 8.10811
88 1DRJ RIP 8.11808
89 1G2O IMH 8.20895
90 2RIF AMP 8.51064
91 4JLS 3ZE 8.55263
92 5GVR LMR 8.64198
93 1LVW TYD 8.64198
94 1H5R THM 8.64198
95 5X20 AOT 8.64198
96 1H5S TMP 8.64198
97 1H5T TYD 8.64198
98 2JBM SRT 8.69565
99 5X80 SAL 8.75
100 5SVV FMN 8.75912
101 1UOU CMU 8.78788
102 4E28 9MZ 9.25926
103 1M7G AV2 9.25926
104 1NE6 SP1 9.25926
105 4OHB 5HM 9.25926
106 4E28 0MZ 9.25926
107 5CGE 51F 9.25926
108 4DE3 DN8 9.39394
109 4GCZ FMN 9.69697
110 4CQ5 TCA 9.87654
111 5MWE TCE 10
112 1EYR CDP 10.0877
113 1BG2 ADP 10.1538
114 2BOS GLA GAL 10.2941
115 2BOS GLA GAL GLC 10.2941
116 4K47 WMP 10.4167
117 5BN3 ADP 10.4938
118 2PZ8 APC 10.5634
119 2QEN ADP 11.1111
120 2C9O ADP 11.1111
121 3P7N FMN 11.1111
122 3O7J 2AL 11.1111
123 1SZ2 BGC 11.1446
124 3RF4 FUN 11.2069
125 4LRZ ADP 11.3744
126 3PNL ADP 11.3744
127 2W58 ADP 11.3861
128 6C0B PAM 11.5385
129 3NY4 SMX 11.6981
130 5ZXD ATP 11.7284
131 1X9I G6Q 11.7284
132 6D56 FVM 11.7284
133 4XRZ SI6 11.7284
134 3SQG COM 12.3457
135 4E03 ADP 12.3457
136 4H3P ANP 12.3457
137 1NU4 MLA 12.3711
138 5CX6 CDP 12.4242
139 5EQ8 HSO 12.7273
140 2O1O RIS 12.963
141 3ZG6 APR 12.963
142 4CNK MEU 13.0435
143 4K6B GLU 13.0435
144 3O5N BR0 13.3929
145 4XH0 ADP 13.3995
146 4QAG F95 13.5338
147 4WEY EG6 13.5802
148 2QHV OC9 13.5802
149 1P6O HPY 13.6646
150 1NBU PH2 14.2857
151 4LO2 GAL BGC 14.2857
152 1M26 GAL A2G 14.2857
153 3ZZH NLG 14.3322
154 4BQS K2Q 14.7727
155 2H6B 3C4 14.8
156 5IRN ADP 14.8148
157 1APZ ASP 14.8148
158 6CWH 6LA 14.8352
159 1JJ7 ADP 15.3846
160 4RI1 ACO 15.4321
161 2YPI PGA 15.7895
162 2FLI DX5 16.0494
163 4G9N NGA 16.0839
164 1US5 GLU 16.6667
165 1O5O U5P 16.7421
166 1GXS BEZ 17.0886
167 1WK8 VMS 17.9012
168 5C8W PCG 18.1818
169 1BHX ASP PHE GLU GLU ILE 18.3673
170 3N8K D1X 19.7674
171 5A0U CHT 21.6049
172 3LL2 MAN MAN MAN MAN MAN MAN MAN MAN 24.3902
173 4RZ3 ADP 24.6914
174 3AB4 THR 27.7778
175 1FIQ MTE 45.0617
176 1FIQ SAL 45.0617
177 1V97 MTE 45.0617
178 3NRZ MTE 48.1481
179 3NRZ HPA 48.1481
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