Receptor
PDB id Resolution Class Description Source Keywords
3PN4 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PETIDE DEFORMYLASE (ATPDF1B) IN COMPLEX WITH ACTINONIN (CRYSTALLIZED IN PEG-55 ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B PDF N-TERMINAL EXCISION PATHWAY NINDUCED-FIT HYDROLASE-ANTIBIOTIC COMPLEX
Ref.: TRAPPING CONFORMATIONAL STATES ALONG LIGAND-BINDING OF PEPTIDE DEFORMYLASE: THE IMPACT OF INDUCED FIT O CATALYSIS. PLOS BIOL. V. 9 E1001 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:501;
Valid;
none;
Kd = 140 nM
385.498 C19 H35 N3 O5 CCCCC...
ZN A:1001;
A:1002;
A:1003;
A:1004;
A:1005;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3M6P 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLAS (ATPDF1B) IN COMPLEX WITH ACTINONIN ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B PDF N-TERMINAL EXCISION PATHWAY NARABIDOPSIS THALIANA INDUCED-FIT HYDROLASE METAL-BINDINGMITOCHONDRION PROTEIN BIOSYNTHESIS TRANSIT PEPTIDE HYDROANTIBIOTIC COMPLEX
Ref.: TRAPPING CONFORMATIONAL STATES ALONG LIGAND-BINDING OF PEPTIDE DEFORMYLASE: THE IMPACT OF INDUCED FIT O CATALYSIS PLOS BIOL. V. 9 01066 2011
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 3PN4 Kd = 140 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
4 3PN3 Ki = 400 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
5 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 3PN4 Kd = 140 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
4 3PN3 Ki = 400 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
5 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3PN4 Kd = 140 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 3PN3 Ki = 400 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BB2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BB2 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3M6P; Ligand: BB2; Similar sites found: 93
This union binding pocket(no: 1) in the query (biounit: 3m6p.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Q3A NGH 0.00001058 0.56065 None
2 4DD8 BAT 0.00001021 0.46857 None
3 5UGW GSH 0.002225 0.45099 None
4 2GBB CIT 0.005452 0.42732 None
5 3JUT GTQ 0.009694 0.42678 None
6 5C2N NAG 0.01689 0.40841 None
7 4WG0 CHD 0.02057 0.40557 None
8 2P4T NAP 0.01265 0.40504 None
9 2TCL RO4 0.00002527 0.48788 1.18343
10 1MMQ RRS 0.00004333 0.49794 1.76471
11 5V4R MGT 0.003189 0.43913 1.85185
12 3KO0 TFP 0.00438 0.44739 1.9802
13 4LO6 SIA GAL 0.02257 0.40728 2.07254
14 1D6Z HY1 0.01593 0.40296 2.07254
15 2P0D I3P 0.004202 0.41627 2.32558
16 2Z9I GLY ALA THR VAL 0.01035 0.42816 2.59067
17 2DC1 CIT 0.02124 0.40229 2.59067
18 4GAA BES 0.0002671 0.46855 3.10881
19 3B9Z CO2 0.00399 0.44858 3.10881
20 1J78 OLA 0.002869 0.42197 3.10881
21 2ZXG S23 0.000227 0.4163 3.10881
22 4IJ6 SEP 0.02252 0.40364 3.10881
23 1UY4 XYP XYP XYP XYP 0.01338 0.41636 3.44828
24 1BKC INN 0.000007825 0.55109 3.62694
25 1KUK PCA LYS TRP 0.000004288 0.51376 3.62694
26 3HY9 098 0.00001522 0.50657 3.62694
27 1FBL HTA 0.000009065 0.49046 3.62694
28 4AR8 IP8 GLY PRO ALA 0.0001003 0.48751 3.62694
29 2FV5 541 0.00002504 0.42182 3.62694
30 3V78 ET 0.005082 0.41964 3.62694
31 1RZM E4P 0.02348 0.40455 3.62694
32 4QHP 32Q 0.002181 0.40379 3.62694
33 3DWB RDF 0.0128 0.40082 3.62694
34 3I7V B4P 0.001594 0.49908 3.73134
35 3KP6 SAL 0.01432 0.40612 3.97351
36 1RM8 BAT 0.00004521 0.53745 4.14201
37 1R55 097 0.00002731 0.54041 4.14508
38 2W14 WR2 0.00003296 0.51531 4.14508
39 1KAP GLY SER ASN SER 0.001412 0.44566 4.14508
40 1Y79 LYS TRP 0.002803 0.44155 4.14508
41 1GEG GLC 0.01684 0.43747 4.14508
42 1PNF NDG NAG 0.007683 0.42992 4.14508
43 2YIV YIV 0.009918 0.4221 4.14508
44 3ZJX BOG 0.01093 0.41907 4.14508
45 1ZPD CIT 0.02689 0.40005 4.14508
46 2V57 PRL 0.01482 0.41124 4.21053
47 4WKI 3PW 0.00001109 0.54401 4.66321
48 2OUA AES 0.01075 0.42532 4.78723
49 3ZVS MLI 0.0007089 0.45101 5
50 4V3I ASP LEU THR ARG PRO 0.01935 0.40871 5.05837
51 2QRD ADP 0.009715 0.40257 5.10949
52 1YP1 LYS ASN LEU 0.000006851 0.57882 5.18135
53 1TE2 PGA 0.002552 0.45272 5.18135
54 3O01 DXC 0.001183 0.44597 5.18135
55 4XMF HSM 0.0164 0.42574 5.43478
56 4WZV E40 0.00009861 0.43463 5.625
57 3CV2 COA 0.007157 0.43265 5.69948
58 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.008643 0.40117 5.69948
59 3UEC ALA ARG TPO LYS 0.004944 0.43266 6.16438
60 3KIH GDL 0.02078 0.40283 6.18557
61 1ATL 0QI 0.0000154 0.52762 6.21762
62 3Q2H QHF 0.000008046 0.51841 6.21762
63 1TL2 NDG 0.009486 0.42015 6.21762
64 1J1R ADE 0.01488 0.41286 6.21762
65 4C2C ALA ALA ALA 0.002319 0.44466 6.73575
66 2YFB SIN 0.01084 0.40973 6.73575
67 1YXM ADE 0.01506 0.40906 6.73575
68 2P3V SRT 0.01814 0.40794 6.73575
69 4C2G ALA ALA ALA ALA 0.01885 0.4007 6.73575
70 2J83 BAT 0.00001549 0.49613 7.25389
71 4L8F MTX 0.01276 0.41832 7.25389
72 4F8L AES 0.04999 0.40084 7.58621
73 4ARF IP8 GLY PRO ALA 0.0004816 0.45714 7.77202
74 4B52 RDF 0.004659 0.41718 7.77202
75 3DBK RDF 0.003882 0.40623 7.77202
76 4DV8 0LX 0.00007772 0.51562 8.29016
77 2XQ0 BES 0.0004175 0.48221 8.29016
78 4KX8 L2O VAL VAL ASP 0.001155 0.4208 8.29016
79 4UP4 NDG 0.02726 0.40054 8.29016
80 2WMC MGP 0.01647 0.42785 8.42697
81 4IN9 SER TRP PHE PRO 0.0005187 0.48801 8.43373
82 1WLJ U5P 0.02548 0.40056 8.46561
83 3AQT RCO 0.01641 0.41071 8.80829
84 1QJI PKF 0.008565 0.40135 9.32642
85 4TV1 36M 0.01065 0.41761 9.84456
86 4MGA 27L 0.01908 0.40723 9.84456
87 5CX6 CDP 0.01373 0.41417 11.399
88 5EHR 5OD 0.009643 0.4066 13.9896
89 2J9L ATP 0.01117 0.41655 14.0541
90 4AIG FLX 0.00004179 0.524 18.6528
91 2YLN CYS 0.005235 0.43838 21.2435
92 5C2F JTH 0.01918 0.40475 28.4974
93 3H0L ADP 0.008281 0.41837 29.7872
Pocket No.: 2; Query (leader) PDB : 3M6P; Ligand: BB2; Similar sites found: 8
This union binding pocket(no: 2) in the query (biounit: 3m6p.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3HBV ALA LYS ALA SER GLN ALA ALA 0.001197 0.44674 3.10881
2 1TDF FAD 0.04044 0.40146 3.10881
3 1MRH FMC 0.02056 0.40115 3.10881
4 1H8P PC 0.004743 0.42636 3.66972
5 3IT6 ORN 0.02203 0.40179 4.14508
6 3V1S 0LH 0.01769 0.40898 4.66321
7 1T3D CYS 0.02759 0.4011 6.21762
8 5IDM C2E 0.004361 0.4816 12.8492
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