Receptor
PDB id Resolution Class Description Source Keywords
4DR9 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCU ELONGATUS IN COMPLEX WITH ACTINONIN SYNECHOCOCCUS ELONGATUS HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND FUNCTION OF A CYANOPHAGE-ENCODED PEPT DEFORMYLASE. ISME J V. 7 1150 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN C:201;
B:201;
D:201;
A:201;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
BB2 B:203;
C:204;
D:203;
A:203;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 10 nM
385.498 C19 H35 N3 O5 CCCCC...
BR C:203;
D:202;
B:202;
C:202;
A:202;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
79.904 Br [Br-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DR9 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCU ELONGATUS IN COMPLEX WITH ACTINONIN SYNECHOCOCCUS ELONGATUS HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND FUNCTION OF A CYANOPHAGE-ENCODED PEPT DEFORMYLASE. ISME J V. 7 1150 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 1WS1 Ki = 0.28 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 1BS8 - MET ALA SER n/a n/a
4 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
5 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
6 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
7 1BS6 - MET ALA SER n/a n/a
8 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
9 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
10 3UWB ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 1RL4 ic50 = 130 nM BL5 C38 H62 N8 O4 CCCC[C@@H]....
12 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
13 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
15 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
16 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
17 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
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 : 4DR9; Ligand: BB2; Similar sites found: 128
This union binding pocket(no: 1) in the query (biounit: 4dr9.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Q3A NGH 0.000005663 0.50182 None
2 1UO5 PIH 0.005946 0.45556 None
3 2OUA AES 0.01091 0.42338 None
4 1UY4 XYP XYP XYP XYP 0.01894 0.40452 None
5 3WV1 WHH 0.000118 0.5217 1.16959
6 4DV8 0LX 0.00004714 0.53156 1.5625
7 3R9V DXC 0.004767 0.43695 1.5625
8 5A0R ACE GLU VAL ASN PRO 0.01341 0.40556 1.5625
9 3PE2 E1B 0.03875 0.40004 1.5625
10 5UGW GSH 0.0009958 0.49179 1.71429
11 3SQP 3J8 0.01052 0.42039 2.08333
12 3SP6 IL2 0.008795 0.40276 2.08333
13 1ATL 0QI 0.000004851 0.55677 2.60417
14 4AIG FLX 0.00001958 0.49057 2.60417
15 4AR8 IP8 GLY PRO ALA 0.00008491 0.48811 2.60417
16 4B52 RDF 0.002403 0.41779 2.60417
17 4RHP PEF 0.006277 0.40531 2.60417
18 5V4R MGT 0.00008602 0.52669 3.08642
19 2ZXG S23 0.00008422 0.50624 3.125
20 4ARF IP8 GLY PRO ALA 0.0004687 0.45526 3.125
21 4WZV E40 0.0000291 0.44628 3.125
22 4A7W GTP 0.02405 0.40585 3.125
23 1N8V BDD 0.01895 0.4047 3.57143
24 2YIP YIO 0.01096 0.41859 3.62319
25 4DD8 BAT 0.000008515 0.4813 3.64583
26 2Z9I GLY ALA THR VAL 0.007323 0.43413 3.64583
27 4PJT 2YQ 0.009344 0.41691 3.64583
28 4WGF HX2 0.01486 0.40305 3.64583
29 5DCH 1YO 0.02087 0.4026 3.64583
30 3GKJ HC3 0.01086 0.40044 3.64583
31 1ZVX FIN 0.0000509 0.52997 3.68098
32 1HFS L04 0.00004869 0.5278 3.75
33 2ED4 FAD 0.01654 0.40263 4.02685
34 2W14 WR2 0.00001643 0.51067 4.16667
35 1R55 097 0.00002574 0.4761 4.16667
36 3TDC 0EU 0.01238 0.45425 4.16667
37 4RW3 TDA 0.002757 0.4467 4.16667
38 1KAP GLY SER ASN SER 0.000476 0.43892 4.16667
39 3H0A D30 0.005584 0.42334 4.16667
40 3LXI CAM 0.008381 0.4231 4.16667
41 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.007538 0.41833 4.16667
42 1B7H LYS NLE LYS 0.01092 0.41731 4.16667
43 3ZJX BOG 0.01136 0.41599 4.16667
44 1R5L VIV 0.008704 0.41141 4.16667
45 5NJI 8Z2 0.01117 0.40927 4.16667
46 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.005434 0.40809 4.16667
47 4RW3 PLM 0.03258 0.40535 4.16667
48 3W68 VIV 0.01064 0.40424 4.16667
49 4COL DTP 0.007301 0.4024 4.16667
50 4IN9 SER TRP PHE PRO 0.0002455 0.40539 4.21687
51 5CHR 4NC 0.003645 0.4423 4.37956
52 3NFD COA 0.01077 0.41073 4.57516
53 3Q2H QHF 0.000002896 0.52903 4.6875
54 2J83 BAT 0.00001597 0.52834 4.6875
55 4KX8 L2O VAL VAL ASP 0.0001416 0.48559 4.6875
56 4GAA BES 0.0001677 0.47502 4.6875
57 3HBV ALA LYS ALA SER GLN ALA ALA 0.00008071 0.47223 4.6875
58 3DBK RDF 0.002137 0.43038 4.6875
59 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.0112 0.42418 4.6875
60 1YKD CMP 0.004522 0.41375 4.6875
61 1XM4 PIL 0.008082 0.40816 4.77387
62 1XMU ROF 0.008224 0.40385 4.77387
63 3ZVS MLI 0.001003 0.4118 5
64 1YP1 LYS ASN LEU 0.000003293 0.49568 5.20833
65 2XQ0 BES 0.0004379 0.42538 5.20833
66 1OUK 084 0.04278 0.42331 5.20833
67 2RCU BUJ 0.02151 0.41901 5.20833
68 4P6X HCY 0.01138 0.41528 5.20833
69 5UC9 MYR 0.02021 0.40305 5.20833
70 1MMQ RRS 0.000009583 0.51764 5.29412
71 3B9Z CO2 0.003289 0.45688 5.72917
72 4ORM ORO 0.02616 0.42057 5.72917
73 4ORM 2V6 0.02616 0.42057 5.72917
74 4ORM FMN 0.02616 0.42057 5.72917
75 4RC8 STE 0.008426 0.40889 5.72917
76 3KPB SAM 0.009173 0.40001 5.7377
77 1JGS SAL 0.0001167 0.4977 5.7971
78 3KO0 TFP 0.005634 0.43762 5.94059
79 3I7V B4P 0.002754 0.46377 5.97015
80 1GEG GLC 0.01531 0.44133 6.25
81 5CX6 CDP 0.01079 0.41763 6.25
82 3G4G D71 0.008198 0.40414 6.25
83 3G58 988 0.008908 0.40058 6.25
84 3GWT 066 0.02202 0.40042 6.25
85 3KP6 SAL 0.01041 0.41537 6.62252
86 4ZW3 4S9 0.00005917 0.52685 6.77083
87 1BKC INN 0.000005661 0.52025 6.77083
88 2FV5 541 0.000002608 0.4443 6.77083
89 4UCC ZKW 0.01254 0.42289 6.77083
90 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.01628 0.40669 6.77083
91 1NF8 BOG 0.02544 0.40288 6.77083
92 4NAT ADP 0.04131 0.41811 6.875
93 1RM8 BAT 0.00002859 0.46403 7.10059
94 4QHP 32Q 0.0007087 0.45606 7.29167
95 3CV2 COA 0.006341 0.42323 7.29167
96 5HCN DAO 0.01962 0.40219 7.29167
97 1BWO LPC 0.006711 0.40805 7.77778
98 2V3V MGD 0.02973 0.42219 7.8125
99 3KH5 AMP 0.02134 0.41697 7.8125
100 1J78 OLA 0.004899 0.41498 7.8125
101 2VWA PTY 0.003694 0.44881 7.92079
102 3HY9 098 0.000004203 0.55178 8.33333
103 3WCA FPS 0.01899 0.40108 8.76712
104 2IV2 MGD 0.005135 0.43643 8.85417
105 1FBL HTA 0.00001199 0.49873 9.375
106 4TV1 36M 0.005372 0.43057 9.375
107 1VPD TLA 0.01 0.42161 9.89583
108 2V5E SCR 0.001259 0.47683 9.90099
109 2TCL RO4 0.000008388 0.54097 10.0592
110 3AHO 3A2 0.001833 0.44265 10.4167
111 4IGH FMN 0.03542 0.41434 10.4167
112 4IGH ORO 0.03542 0.41434 10.4167
113 4IGH 1EA 0.03542 0.41434 10.4167
114 5EHR 5OD 0.01178 0.40052 10.4167
115 2FP2 TSA 0.007202 0.40667 10.8434
116 1KUK PCA LYS TRP 0.00001592 0.50218 11.4583
117 2GBB CIT 0.002613 0.40037 11.5385
118 3KXC PLM 0.01242 0.40426 12.0253
119 4K90 MLA 0.02055 0.4031 12.5
120 4WKI 3PW 0.00001474 0.5354 13.0208
121 5OCA 9QZ 0.00847 0.43316 15.1042
122 2QZT PLM 0.003205 0.43605 17.1171
123 1OFD FMN 0.02345 0.40348 18.2292
124 1OFD AKG 0.02119 0.40348 18.2292
125 2Y69 CHD 0.01178 0.41489 20.6349
126 3EE4 MYR 0.006477 0.41241 21.3542
127 2OBD PCW 0.0154 0.40662 22.3958
128 5MWE TCE 0.01653 0.40596 24.6914
Pocket No.: 2; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 4dr9.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WMC MGP 0.01386 0.43169 None
2 3SE5 ANP 0.005163 0.40908 None
3 2ALG DAO 0.01037 0.4031 None
4 2ALG HP6 0.01037 0.4031 None
5 3WLV AZA 0.01889 0.40302 1.04167
6 2HFP NSI 0.01163 0.40406 1.5625
7 3T03 3T0 0.006823 0.4037 1.5625
8 4XMF HSM 0.02652 0.401 1.63043
9 4JNA FAD 0.0205 0.41296 2.08333
10 2CHT TSA 0.01882 0.4031 2.3622
11 3WYJ H78 0.01969 0.42693 2.60417
12 4UP4 NAG 0.02741 0.4004 2.60417
13 4UP4 NDG 0.02741 0.4004 2.60417
14 1SQL GUN 0.0209 0.40611 3.42466
15 3NYQ MCA 0.01286 0.41275 4.16667
16 3NYQ AMP 0.01384 0.41238 4.16667
17 1N4W FAD 0.02763 0.40738 4.16667
18 1EJ4 M7G 0.02468 0.40212 4.21053
19 2Y7P SAL 0.01307 0.41111 4.6875
20 1TE2 PGA 0.001078 0.47143 5.20833
21 4YMX ARG 0.005837 0.41912 5.20833
22 4OYA 1VE 0.03111 0.41608 5.20833
23 3KFC 61X 0.0189 0.40241 5.72917
24 4CZG QH3 0.02257 0.40429 6.25
25 5X8G S0N 0.02541 0.41161 8.33333
26 3V78 ET 0.01058 0.40271 9.375
27 3KDU NKS 0.01516 0.42283 10.9375
28 2ZCQ B65 0.0373 0.40005 11.4583
29 1FEC FAD 0.03473 0.4048 11.9792
30 2FN1 PYR 0.01677 0.4128 14.0625
31 3R1V AZB 0.01504 0.4004 16.5354
32 5L2J 6UL 0.03926 0.41143 17.3469
33 2QQD AG2 0.01708 0.40524 21.4286
34 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.009874 0.40821 22.8571
35 5BSR COA 0.03985 0.4074 28.125
36 5BSR AMP 0.0255 0.4074 28.125
Pocket No.: 3; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found: 23
This union binding pocket(no: 3) in the query (biounit: 4dr9.bio4) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IDC NDP 0.02805 0.4008 None
2 4IDC 1XX 0.02805 0.4008 None
3 3G9E RO7 0.02409 0.40406 1.5625
4 2BIF BOG 0.01106 0.40542 2.08333
5 2E2R 2OH 0.02942 0.40084 2.08333
6 5V3Y 5V8 0.004506 0.40118 2.60417
7 2HW2 RFP 0.01565 0.40001 2.7972
8 2A1L PCW 0.03133 0.40695 3.125
9 1YOK P6L 0.02339 0.40681 3.125
10 4ZOM 4Q3 0.03646 0.42007 3.64583
11 4E5N NAD 0.01845 0.40747 3.64583
12 4QOM PYG 0.01186 0.40228 3.64583
13 1LLF F23 0.02297 0.40821 5.20833
14 3EWC MCF 0.01599 0.4026 7.29167
15 2Z7I 742 0.04408 0.41349 7.8125
16 2I0G I0G 0.0435 0.40432 7.8125
17 4QWT ACD 0.01865 0.40085 8.33333
18 4YJK URA 0.01713 0.40268 8.85417
19 3DWB RDF 0.005005 0.40554 9.89583
20 3T3C 017 0.01748 0.4049 14.1414
21 2P3C 3TL 0.02494 0.40742 16.1616
22 3HUJ AGH 0.04842 0.40118 17.1717
23 4NTC FAD 0.0405 0.40044 19.7917
Pocket No.: 4; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found: 13
This union binding pocket(no: 4) in the query (biounit: 4dr9.bio3) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FKW RG1 0.01851 0.40238 None
2 3FUR Z12 0.04522 0.40043 1.5625
3 3Q8G PEE 0.04441 0.40596 2.08333
4 4CS4 AXZ 0.04336 0.40057 2.60417
5 1QJI PKF 0.006951 0.40717 3.125
6 1HSR BHO 0.01321 0.40989 4.16667
7 3Q9T FAY 0.02627 0.40724 4.16667
8 1XVB 3BR 0.01175 0.4025 4.6875
9 1FIQ SAL 0.02205 0.40484 6.25
10 2AX9 BHM 0.03816 0.4 6.25
11 1P0F NAP 0.0168 0.41062 7.29167
12 5G3N X28 0.01098 0.40558 10.2362
13 2ZWA SAH 0.01504 0.40082 18.2292
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