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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:194;
B:194;
Valid;
Valid;
none;
none;
Kd = 0.9 nM
385.498 C19 H35 N3 O5 CCCCC...
ZN A:195;
A:196;
A:197;
A:198;
A:199;
B:195;
B:196;
B:197;
B:198;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
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 (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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....
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 with APoc: 178
This union binding pocket(no: 1) in the query (biounit: 3m6p.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4DD8 BAT None
2 1Q3A NGH None
3 1NU4 MLA None
4 5UGW GSH None
5 2GBB CIT None
6 3K1X DBX None
7 3NFD COA None
8 1R6N 434 None
9 4WG0 CHD None
10 4GK9 MAN BMA MAN MAN MAN None
11 5C2N NAG None
12 2P4T NAP None
13 2P4Y C03 None
14 1MID LAP None
15 2TCL RO4 1.18343
16 4TMN 0PK 1.5544
17 6BVE PGA 1.5544
18 1MMQ RRS 1.76471
19 1ZVX FIN 1.84049
20 5V4R MGT 1.85185
21 3KO0 TFP 1.9802
22 5O2N FLC 2.07254
23 4LO6 SIA GAL 2.07254
24 1D6Z HY1 2.07254
25 2P0D I3P 2.32558
26 3KPB SAM 2.45902
27 1HFS L04 2.5
28 2Z9I GLY ALA THR VAL 2.59067
29 3GD8 GOL 2.59067
30 3C88 ARG ARG GLY CYS NH2 2.59067
31 2DC1 CIT 2.59067
32 6BTN E8M 2.59067
33 3WV1 WHH 2.92398
34 4GAA BES 3.10881
35 2ZXG S23 3.10881
36 3B9Z CO2 3.10881
37 1J78 OLA 3.10881
38 3AB1 FAD 3.10881
39 4IJ6 SEP 3.10881
40 4BQS K2Q 3.40909
41 4BQS ADP 3.40909
42 1UY4 XYP XYP XYP XYP 3.44828
43 1KUK PCA LYS TRP 3.62694
44 1FBL HTA 3.62694
45 1BKC INN 3.62694
46 4AR8 IP8 GLY PRO ALA 3.62694
47 5C9J DAO 3.62694
48 5DUF G7A 3.62694
49 2FV5 541 3.62694
50 3V78 ET 3.62694
51 5ME4 HP4 3.62694
52 3W54 RNB 3.62694
53 1RZM E4P 3.62694
54 4QHP 32Q 3.62694
55 1RJW ETF 3.62694
56 3DWB RDF 3.62694
57 3WLV AZA 3.62694
58 3I7V B4P 3.73134
59 3KP6 SAL 3.97351
60 1SQL GUN 4.10959
61 1RM8 BAT 4.14201
62 2W14 WR2 4.14508
63 1R55 097 4.14508
64 1ZED PNP 4.14508
65 1KAP GLY SER ASN SER 4.14508
66 1Y79 LYS TRP 4.14508
67 1GEG GLC 4.14508
68 1PNF NDG NAG 4.14508
69 2YIV YIV 4.14508
70 3ZJX BOG 4.14508
71 3D3X ARG ILE MET GLU NH2 4.14508
72 4WGF HX2 4.14508
73 5NM7 GLY 4.14508
74 2RCU BUJ 4.14508
75 1ZPD CIT 4.14508
76 2V57 PRL 4.21053
77 4WKI 3PW 4.66321
78 4ZW3 4S9 4.66321
79 2VJ8 HA2 4.66321
80 1B4N GUA 4.66321
81 6MVU K4V 4.66321
82 3E8T UQ8 4.66321
83 3UYW TAU 4.66321
84 5H0U HIS HIS HIS HIS HIS HIS 4.70588
85 2OUA AES 4.78723
86 3ZVS MLI 5
87 4V3I ASP LEU THR ARG PRO 5.05837
88 2QRD ADP 5.10949
89 1YP1 LYS ASN LEU 5.18135
90 2GWH PCI 5.18135
91 1TE2 PGA 5.18135
92 3O01 DXC 5.18135
93 3AHO 3A2 5.18135
94 2V3V MGD 5.18135
95 5ZRR 9J3 5.18135
96 4WVH ASP HIS ASP ALA HIS ALA 5.25328
97 2ED4 FAD 5.36913
98 4XMF HSM 5.43478
99 4WZV E40 5.625
100 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 5.69948
101 5WBF LAC 5.69948
102 4CA5 3EF 5.69948
103 3CV2 COA 5.69948
104 6H8S FSZ 5.69948
105 5KDS A2G THR ALA PRO GLY GLY NAG SIA 5.69948
106 1NE7 16G 5.69948
107 4YRY NAD 5.69948
108 3UEC ALA ARG TPO LYS 6.16438
109 3KIH GDL 6.18557
110 1ATL 0QI 6.21762
111 3Q2H QHF 6.21762
112 2YB9 HA0 6.21762
113 5OSW DIU 6.21762
114 1J1R ADE 6.21762
115 1TL2 NDG 6.21762
116 5ECP MET 6.21762
117 5ECP ATP 6.21762
118 5ECP JAA 6.21762
119 4YV5 SVR 6.55738
120 4C2C ALA ALA ALA 6.73575
121 2YFB SIN 6.73575
122 1YXM ADE 6.73575
123 2P3V SRT 6.73575
124 5HI5 63Q 6.73575
125 6BSW UDP 6.73575
126 4C2G ALA ALA ALA ALA 6.73575
127 2NV2 GLN 6.73575
128 2I0K FAD 6.73575
129 2J83 BAT 7.25389
130 4L8F MTX 7.25389
131 6AYU MLI 7.25389
132 1YQS BSA 7.25389
133 4RJD TFP 7.57576
134 5O7E 9NB 7.77202
135 2R4J FAD 7.77202
136 2R4J 13P 7.77202
137 4B52 RDF 7.77202
138 4DV8 0LX 8.29016
139 4KX8 L2O VAL VAL ASP 8.29016
140 4BXK 1IU 8.29016
141 2XQ0 BES 8.29016
142 4UP4 NDG 8.29016
143 2WMC MGP 8.42697
144 4IN9 SER TRP PHE PRO 8.43373
145 1WLJ U5P 8.46561
146 6BMN PAP 8.80829
147 3AQT RCO 8.80829
148 2UUU FAD 8.80829
149 2UUU PL3 8.80829
150 1M2Z BOG 8.80829
151 2UW1 GVM 9.32642
152 1P4V GLY 9.32642
153 1QJI PKF 9.32642
154 4TV1 36M 9.84456
155 5BSR COA 9.84456
156 5BSR AMP 9.84456
157 1G8K MGD 9.84456
158 4MGA 27L 9.84456
159 3KIF GDL 11.3208
160 5CX6 CDP 11.399
161 5MZI FYK 12.4352
162 4OGQ 2WD 13.4715
163 2J9L ATP 14.0541
164 2Y69 CHD 14.2857
165 1VAY AZA 15.544
166 5C9P FUC 17.0984
167 4AIG FLX 18.6528
168 5Z84 CHD 19.1489
169 5ZCO CHD 19.1489
170 5W97 CHD 19.1489
171 4CZG ADP 19.5402
172 5YZ2 AMP 20.8333
173 2YLN CYS 21.2435
174 5ZI7 GLU 23.8342
175 5C2F JTH 28.4974
176 3H0L ADP 29.7872
177 5NNT DPV 32.4324
178 5MTE BB2 44.5255
Pocket No.: 2; Query (leader) PDB : 3M6P; Ligand: BB2; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 3m6p.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3ENV ABF 1.5544
2 3HBV ALA LYS ALA SER GLN ALA ALA 3.10881
3 1TDF FAD 3.10881
4 1MRH FMC 3.10881
5 3AKI AH8 3.62694
6 5WXU FLC 3.62694
7 1H8P PC 3.66972
8 3NOJ PYR 4.14508
9 6DQU GLY ILE ILE ASN THR LEU 4.14508
10 2V58 LZJ 4.14508
11 3IT6 ORN 4.14508
12 5T63 ALA ALA ALA ALA 4.66321
13 3V1S 0LH 4.66321
14 4QOM PYG 5.69948
15 3KH5 ADP 5.69948
16 3KH5 AMP 5.69948
17 4XTX 590 6.21762
18 1T3D CYS 6.21762
19 1B7H LYS NLE LYS 7.25389
20 1PVC ILE SER GLU VAL 7.25389
21 4F8L AES 7.58621
22 1C9K 5GP 8.33333
23 1H2B NAJ 9.84456
24 3ZXR P3S 11.399
25 3ZXR IQ1 11.399
26 5IDM C2E 12.8492
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