Receptor
PDB id Resolution Class Description Source Keywords
5K53 1.8 Å EC: 1.-.-.- CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM OSCILLATORIA SP. KNUA011 OSCILLATORIA SP. FERRITIN-LIKE DI-IRON PROTEIN METAL BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGEN LIMNOTHRIX SP. KNUA012 AND OSCILLATORIA SP. KNUA011 BIOCHEM.BIOPHYS.RES.COMMUN. V. 477 395 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:501;
A:500;
B:500;
B:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
55.845 Fe [Fe+3...
STE A:502;
B:502;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.05;
Atoms found LESS than expected: % Diff = 0.05;
submit data
284.477 C18 H36 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K53 1.8 Å EC: 1.-.-.- CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM OSCILLATORIA SP. KNUA011 OSCILLATORIA SP. FERRITIN-LIKE DI-IRON PROTEIN METAL BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGEN LIMNOTHRIX SP. KNUA012 AND OSCILLATORIA SP. KNUA011 BIOCHEM.BIOPHYS.RES.COMMUN. V. 477 395 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 5K53 - STE C18 H36 O2 CCCCCCCCCC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 5K53 - STE C18 H36 O2 CCCCCCCCCC....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4PG1 - Y39 C13 H24 O2 CCCCCCCCC[....
2 4PGK - Y69 C17 H34 O4 CCOCCOCCOC....
3 4PGI - Y69 C17 H34 O4 CCOCCOCCOC....
4 4TW3 - STE C18 H36 O2 CCCCCCCCCC....
5 4PG0 - Y39 C13 H24 O2 CCCCCCCCC[....
6 4KVS - 6NA C6 H12 O2 CCCCCC(=O)....
7 4KVQ - PLM C16 H32 O2 CCCCCCCCCC....
8 4KVR - 6NA C6 H12 O2 CCCCCC(=O)....
9 5K53 - STE C18 H36 O2 CCCCCCCCCC....
10 4RC7 - PL3 C16 H34 O CCCCCCCCCC....
11 4QUW - PL3 C16 H34 O CCCCCCCCCC....
12 4RC5 - PL3 C16 H34 O CCCCCCCCCC....
13 4RC8 - STE C18 H36 O2 CCCCCCCCCC....
14 5K52 - OCD C18 H36 O CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: STE; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K53; Ligand: STE; Similar sites found: 130
This union binding pocket(no: 1) in the query (biounit: 5k53.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZFZ ARG 0.02273 0.43048 None
2 2BYC FMN 0.008661 0.41256 None
3 1G27 BB1 0.00535 0.40707 None
4 2I0G I0G 0.008285 0.42739 0.77821
5 3FUR Z12 0.009018 0.4223 1.9084
6 3KDU NKS 0.009817 0.42229 1.9084
7 3G9E RO7 0.006947 0.41633 1.9084
8 1H82 GZZ 0.03125 0.40747 1.9084
9 1H82 FAD 0.02688 0.40747 1.9084
10 1SR7 MOF 0.001441 0.44431 2.3166
11 4OAR 2S0 0.006102 0.40126 2.32558
12 2AX9 BHM 0.007122 0.42236 2.34375
13 1YOK P6L 0.01047 0.41056 2.34375
14 3WYJ H78 0.00869 0.43508 2.37154
15 4URN NOV 0.0275 0.40012 2.66667
16 4ORM FMN 0.01082 0.43048 2.67176
17 4ORM 2V6 0.01082 0.43048 2.67176
18 4ORM ORO 0.01082 0.43048 2.67176
19 3QCQ 3Q0 0.03369 0.41489 2.67176
20 4MGA 27L 0.007984 0.43678 2.7451
21 5AAV GW5 0.006333 0.43605 2.77778
22 2QE4 JJ3 0.03098 0.40103 2.82258
23 5LX9 OLB 0.002142 0.43669 3.05344
24 4OMJ 2TX 0.006817 0.4155 3.05344
25 4MNS 2AX 0.01087 0.42022 3.14465
26 5B4B LP5 0.003367 0.42521 3.43511
27 4X8D AVI 0.01235 0.42117 3.43511
28 3R9V DXC 0.01583 0.41573 3.43511
29 3G5N PB2 0.04148 0.40375 3.43511
30 3RI1 3RH 0.006995 0.40696 3.51438
31 3E85 BSU 0.01344 0.40872 3.79747
32 1GNI OLA 0.01325 0.4621 3.81679
33 5LD8 6U5 0.01552 0.41531 3.81679
34 5XJN 88L 0.008068 0.41402 3.81679
35 1YUC EPH 0.006007 0.40831 3.92157
36 5UC9 MYR 0.01581 0.41535 3.9823
37 4QWT ACD 0.006988 0.40698 4.02299
38 5EW9 5VC 0.008585 0.45073 4.19847
39 2Q2Y MKR 0.02689 0.41684 4.19847
40 2Q2Y ADP 0.02689 0.41684 4.19847
41 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 0.009431 0.40673 4.19847
42 1M2Z BOG 0.002364 0.4578 4.28016
43 5LGA 6VH 0.008735 0.41301 4.33333
44 5E7V M7E 0.007383 0.41014 4.33333
45 3E8T UQ8 0.02805 0.40522 4.54545
46 1TV5 N8E 0.0005359 0.50762 4.58015
47 4LY9 S6P 0.004078 0.43834 4.58015
48 4LY9 1YY 0.004266 0.43834 4.58015
49 3L9R L9R 0.004286 0.42575 4.58015
50 3L9R L9Q 0.006424 0.41786 4.58015
51 3RDE OYP 0.005651 0.40621 4.58015
52 5U9J GER 0.01682 0.41113 4.73373
53 5IR4 ZPE 0.01216 0.41358 4.96183
54 5APJ 76E 0.01112 0.40227 4.96183
55 5NTW 98N 0.01058 0.40451 5.05837
56 3B6C SDN 0.01355 0.41595 5.12821
57 3KXC PLM 0.003752 0.41717 5.15464
58 4IEH 1E9 0.005215 0.40937 5.32544
59 3LN0 52B 0.001791 0.44982 5.34351
60 4Q86 AMP 0.008158 0.40983 5.34351
61 4ZW3 4S9 0.01217 0.40651 5.34351
62 2P1C GG3 0.01213 0.4006 5.34351
63 5IXK 6EW 0.009623 0.40759 5.70175
64 3MBG FAD 0.009691 0.40078 5.7554
65 4ZOM 4Q3 0.01521 0.42745 5.77778
66 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 0.01126 0.40803 5.85774
67 4LWU 20U 0.006213 0.41531 5.88235
68 1QSM ACO 0.007833 0.40481 5.92105
69 4UCC ZKW 0.002314 0.46381 6.00858
70 2XXP DSL 0.0308 0.4107 6.10687
71 4P6X HCY 0.006255 0.41718 6.27451
72 1DB1 VDX 0.007186 0.41448 6.48855
73 3VRV YSD 0.01919 0.40861 6.48855
74 1M13 HYF 0.00614 0.41629 6.64557
75 1N83 CLR 0.006434 0.40702 6.66667
76 2ZCQ B65 0.024 0.40074 6.87023
77 3JUQ AJD 0.006179 0.40454 7.02703
78 3JUQ AKD 0.006748 0.40454 7.02703
79 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 0.009837 0.41592 7.07071
80 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.00816 0.41434 7.07071
81 1LEK GLU GLN TYR LYS PHE TYR SER VAL 0.03852 0.40421 7.07071
82 4OIV XX9 0.008138 0.41869 7.07965
83 2FV5 541 0.01106 0.40365 7.27969
84 5DCH 1YO 0.005979 0.43712 7.29167
85 3PVT 3HC 0.02867 0.41794 7.33591
86 3G08 FEE 0.00127 0.4683 8.01527
87 3SCM LGN 0.005287 0.43977 8.01527
88 4ZBR NPS 0.0107 0.40552 8.01527
89 4ZBR DIF 0.01138 0.40552 8.01527
90 4IGH FMN 0.01853 0.41975 8.39695
91 4IGH ORO 0.01853 0.41975 8.39695
92 4IGH 1EA 0.01853 0.41975 8.39695
93 1LOX RS7 0.002833 0.40116 8.39695
94 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.009549 0.40387 8.40336
95 5CSD ACD 0.004763 0.42604 9.43396
96 4F7E 0SH 0.002098 0.44558 9.54198
97 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.005493 0.44335 10.2041
98 4X6F 3XU 0.002795 0.4399 10.4762
99 1XVB BHL 0.00006073 0.51572 10.687
100 5IF4 6AK 0.009725 0.40352 10.6918
101 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 0.01028 0.4205 11
102 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.0083 0.4183 11
103 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.01308 0.41301 11
104 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.01731 0.40907 11
105 3QKD HI0 0.001083 0.44054 11.0497
106 5U98 1KX 0.001977 0.46242 11.1111
107 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.00422 0.42224 11.1111
108 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 0.003434 0.43362 11.2245
109 5L2J 6UL 0.01127 0.42962 11.2245
110 5L2J 70E 0.01267 0.42841 11.2245
111 3BZF VAL MET ALA PRO ARG ALA LEU LEU LEU 0.005129 0.42225 11.3402
112 4QVX 3CQ 0.00242 0.42018 11.976
113 3PF7 MLA 0.0001771 0.42106 12.2137
114 3F3E LEU 0.01115 0.41141 12.2137
115 3QUZ QUV 0.002041 0.45686 13.278
116 3KFC 61X 0.01259 0.40356 13.834
117 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.007465 0.41987 14.2857
118 3Q8G PEE 0.03232 0.40158 14.5038
119 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.00974 0.41803 14.5299
120 4WT2 3UD 0.007851 0.40761 16.1905
121 4OAS 2SW 0.007169 0.41243 16.6667
122 3ZLR X0B 0.008837 0.41497 17.7215
123 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.00353 0.43193 18.3673
124 5V4R MGT 0.0005363 0.49608 18.5185
125 3D9F FAD 0.02006 0.41076 20.6107
126 3D9F N6C 0.02006 0.41076 20.6107
127 2QQD AG2 0.01966 0.40764 22.6415
128 5OCA 9QZ 0.0000309 0.5734 23.0159
129 1HN4 MJI 0.008131 0.43712 35.8779
130 3EE4 MYR 0.00844 0.42451 37.4046
Pocket No.: 2; Query (leader) PDB : 5K53; Ligand: STE; Similar sites found: 22
This union binding pocket(no: 2) in the query (biounit: 5k53.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FS0 5JC 0.01741 0.40602 1.4218
2 5GWE GWM 0.02207 0.40084 1.9084
3 2J07 HDF 0.03111 0.40021 2.29008
4 2J07 FAD 0.03111 0.40021 2.29008
5 3G5K BB2 0.0107 0.40074 3.82514
6 3TJH SER PRO LEU ASP SER LEU TRP TRP ILE 0.01559 0.40672 3.9823
7 1RTW MP5 0.02368 0.40347 4.09091
8 1YMT DR9 0.008855 0.40531 4.19847
9 3IX9 MTX 0.01547 0.40058 4.21053
10 2YLN CYS 0.02707 0.40252 4.59364
11 5KAX RHQ 0.02345 0.40369 4.81928
12 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.01387 0.41095 4.91803
13 3BPX SAL 0.02049 0.40563 6.10687
14 3H0A D30 0.01016 0.4013 6.14035
15 4CA5 3EF 0.01555 0.41449 6.48855
16 1ZT1 PHE GLU ALA ASN GLY ASN LEU ILE 0.01187 0.40228 7
17 1MO9 FAD 0.04637 0.40696 7.25191
18 4BNU 9KQ 0.00644 0.40377 8.39695
19 2Z7I 742 0.03306 0.40862 9.16031
20 1RSG FAD 0.0209 0.40354 13.3588
21 5AZC PGT 0.00496 0.45476 13.7405
22 4RW3 TDA 0.01127 0.4186 27.4809
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