Receptor
PDB id Resolution Class Description Source Keywords
5K52 2.4 Å EC: 4.1.99.5 CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM SP. KNUA012 LIMNOTHRIX SP. KNUA012 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. V. 477 395 2016 COMMUN.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
OCD A:500;
C:500;
Valid;
Valid;
none;
none;
submit data
268.478 C18 H36 O CCCCC...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K52 2.4 Å EC: 4.1.99.5 CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM SP. KNUA012 LIMNOTHRIX SP. KNUA012 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. V. 477 395 2016 COMMUN.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5K52 - OCD C18 H36 O CCCCCCCCCC....
70% Homology Family (13)
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 4RC7 - PL3 C16 H34 O CCCCCCCCCC....
10 4QUW - PL3 C16 H34 O CCCCCCCCCC....
11 4RC5 - PL3 C16 H34 O CCCCCCCCCC....
12 4RC8 - STE C18 H36 O2 CCCCCCCCCC....
13 5K52 - OCD C18 H36 O 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: OCD; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 UNA 1 1
2 OCD 1 1
3 8YP 1 1
4 OYA 0.954545 1
5 B7M 0.575758 0.75
6 PTL 0.541667 0.714286
7 1EY 0.529412 0.6875
8 TRD 0.5 0.733333
9 UND 0.5 0.733333
10 TWT 0.5 0.733333
11 MYS 0.5 0.733333
12 R16 0.5 0.733333
13 8K6 0.5 0.733333
14 D10 0.5 0.733333
15 LFA 0.5 0.733333
16 C14 0.5 0.733333
17 DD9 0.5 0.733333
18 D12 0.5 0.733333
19 3X1 0.457143 0.65
20 OCT 0.454545 0.733333
21 OLA 0.421053 0.636364
22 NER 0.421053 0.636364
23 ELA 0.421053 0.636364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K52; Ligand: OCD; Similar sites found: 103
This union binding pocket(no: 1) in the query (biounit: 5k52.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FHT DHB 0.005248 0.44193 None
2 2Z9I GLY ALA THR VAL 0.02014 0.41532 0.754717
3 3E3U NVC 0.006524 0.41612 1.01523
4 1M2Z BOG 0.003638 0.4535 1.16732
5 5U9J GER 0.02048 0.40838 1.18343
6 4XVX P33 FDA 0.01244 0.40314 1.50943
7 3PF7 MLA 0.0002673 0.41836 1.88679
8 5VRH OLB 0.02192 0.40908 2.10728
9 5LWY OLB 0.004886 0.42196 2.26415
10 4X8D AVI 0.008221 0.42085 2.26415
11 4IGH ORO 0.0255 0.41033 2.26415
12 4IGH FMN 0.0255 0.41033 2.26415
13 4IGH 1EA 0.0255 0.41033 2.26415
14 1GNI OLA 0.02073 0.44888 2.64151
15 3W54 RNB 0.001013 0.44457 2.64151
16 3HP9 CF1 0.01916 0.40987 2.64151
17 3WUR O4B 0.02064 0.40764 2.92398
18 3G9E RO7 0.005494 0.41768 3.01887
19 1IID NHM 0.01832 0.4007 3.01887
20 1PU7 39A 0.02033 0.40117 3.21101
21 4RQL SNE 0.01191 0.41598 3.39623
22 3F3E LEU 0.01282 0.40574 3.39623
23 4V3I ASP LEU THR ARG PRO 0.005182 0.44714 3.50195
24 3KFC 61X 0.005977 0.41486 3.55731
25 1G27 BB1 0.01007 0.40021 3.57143
26 3SQP 3J8 0.005538 0.4414 3.77358
27 5AZC PGT 0.0122 0.4325 3.77358
28 5L8N 6RQ 0.03336 0.40057 3.77358
29 3QKD HI0 0.007464 0.4011 3.8674
30 5UGW GSH 0.003843 0.41532 4
31 1VPD TLA 0.02576 0.40514 4.15094
32 4UZI IMD 0.03238 0.40456 4.15094
33 1N83 CLR 0.00642 0.40389 4.15094
34 4QVX 3CQ 0.004485 0.40545 4.19162
35 1TV5 N8E 0.000296 0.52058 4.5283
36 4OMJ 2TX 0.005493 0.41647 4.5283
37 1XM4 PIL 0.008129 0.41563 4.5283
38 1XMU ROF 0.009089 0.4094 4.5283
39 5F74 AMP 0.01443 0.41624 4.59184
40 3B6C SDN 0.009669 0.42522 4.70085
41 5KAX RHQ 0.02461 0.40425 4.81928
42 1SR7 MOF 0.002827 0.42781 4.90566
43 5IR4 ZPE 0.00971 0.41507 4.90566
44 3KDU NKS 0.01669 0.40865 4.90566
45 1J78 OLA 0.02178 0.40122 4.90566
46 5B25 4QJ 0.01419 0.40038 4.90566
47 5OFW 9TW 0.02301 0.40806 4.93274
48 2VWA PTY 0.004275 0.43615 4.9505
49 3TDC 0EU 0.01484 0.43979 5.28302
50 2QES ADE 0.03261 0.40164 5.36398
51 4MRP GSH 0.00333 0.46887 5.66038
52 3WYJ H78 0.01008 0.42896 5.66038
53 3TL1 JRO 0.02493 0.40396 6.41509
54 3KP6 SAL 0.006378 0.43216 6.62252
55 3KU0 ADE 0.01841 0.40798 6.77291
56 3G58 988 0.00535 0.42872 6.79245
57 2XN5 FUN 0.01994 0.40073 6.79245
58 2Q4G CIT 0.02845 0.40098 6.97674
59 4HBM 0Y7 0.005214 0.41669 7.5
60 4MNS 2AX 0.008128 0.42305 7.54717
61 2WH8 II2 0.01845 0.40642 7.74818
62 5MES 7LT 0.003645 0.43223 7.82609
63 5UC9 MYR 0.02087 0.41057 7.9646
64 3L9R L9R 0.004427 0.42181 8.16327
65 3L9R L9Q 0.01148 0.40357 8.16327
66 4LWU 20U 0.007985 0.41203 8.23529
67 3BPX SAL 0.02834 0.40483 8.30189
68 5DCH 1YO 0.01865 0.41235 8.33333
69 1SBR VIB 0.01679 0.41285 8.5
70 4UCC ZKW 0.002293 0.47085 8.58369
71 5B4B LP5 0.00404 0.41837 8.67924
72 5EW9 5VC 0.03475 0.4173 8.67924
73 3G5K BB2 0.01137 0.40126 9.28962
74 4ZOM 4Q3 0.03343 0.40802 9.33333
75 4OAS 2SW 0.01288 0.40233 9.375
76 4MGA 27L 0.01434 0.4238 9.41177
77 4MGD 27N 0.01401 0.40063 9.41177
78 4RLT FSE 0.009593 0.4122 9.49367
79 2QE4 JJ3 0.01213 0.41743 9.67742
80 5LX9 OLB 0.00199 0.4401 10.0977
81 5U98 1KX 0.0179 0.40116 10.101
82 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.01121 0.40042 10.101
83 5L2J 70E 0.001992 0.46374 10.2041
84 5L2J 6UL 0.001861 0.46374 10.2041
85 4YSX E23 0.01124 0.42184 10.2564
86 3GXO MQA 0.01994 0.40472 10.5691
87 4O4Z N2O 0.0008043 0.50905 11.039
88 5OCA 9QZ 0.00009715 0.53534 11.0599
89 5FUS DAO 0.01452 0.40359 11.3208
90 3WFD AXO 0.01256 0.40186 12.3288
91 5V4R MGT 0.0003854 0.51129 12.3457
92 5CHR 4NC 0.005107 0.44094 12.4088
93 2CB8 MYA 0.02376 0.40856 12.6437
94 3FAL LO2 0.007921 0.407 12.8099
95 1XXA ARG 0.01121 0.42191 12.8205
96 1XVB BHL 0.00006689 0.50893 13.5849
97 3CHT 4NB 0.002805 0.45653 14.5833
98 3N7S 3N7 0.01927 0.4215 15.6522
99 1RTW MP5 0.01528 0.41496 15.9091
100 3G08 FEE 0.003379 0.44479 20.202
101 3SCM LGN 0.007485 0.42949 20.202
102 5MWE TCE 0.008162 0.42901 25.9259
103 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.008778 0.41821 33.3333
Pocket No.: 2; Query (leader) PDB : 5K52; Ligand: OCD; Similar sites found: 12
This union binding pocket(no: 2) in the query (biounit: 5k52.bio3) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LE7 ADE 0.02738 0.40291 None
2 4DXJ IPE 0.0118 0.40069 1.50943
3 4DXJ 0M9 0.01033 0.40069 1.50943
4 1LQY BB2 0.00151 0.43687 2.17391
5 5IKR ID8 0.005855 0.42243 3.01887
6 4HDK 13X 0.02708 0.40209 3.01887
7 2JHP GUN 0.02183 0.40111 4.15094
8 1YUC EPH 0.009965 0.40266 4.70588
9 5FS0 5JC 0.009025 0.42204 5.6872
10 2BYC FMN 0.01696 0.40035 6.56934
11 2GBB CIT 0.02635 0.40271 10.2564
12 2QQD AG2 0.01644 0.41333 10.7143
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