Receptor
PDB id Resolution Class Description Source Keywords
2OKL 1.7 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE 2 WITH ACTINONIN FR BACILLUS CEREUS BACILLUS CEREUS HYDROLASE
Ref.: CHARACTERIZATION OF PEPTIDE DEFORMYLASE2 FROM B. CE J.BIOCHEM.MOL.BIOL. V. 40 1050 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:401;
A:404;
B:402;
B:403;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
385.498 C19 H35 N3 O5 CCCCC...
CIT A:501;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
ZN A:601;
B:602;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2OKL 1.7 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE 2 WITH ACTINONIN FR BACILLUS CEREUS BACILLUS CEREUS HYDROLASE
Ref.: CHARACTERIZATION OF PEPTIDE DEFORMYLASE2 FROM B. CE J.BIOCHEM.MOL.BIOL. V. 40 1050 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
8 3G6N - MET ALA SER n/a n/a
9 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
12 5JEZ - MET ALA SER n/a n/a
13 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
14 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
15 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
16 5JF0 - MET ALA ARG n/a n/a
17 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
18 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
19 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
20 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
8 3G6N - MET ALA SER n/a n/a
9 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
13 5JEZ - MET ALA SER n/a n/a
14 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
15 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
16 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
17 5JF0 - MET ALA ARG n/a n/a
18 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
19 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
20 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
21 5JF8 Ki = 1428 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 : 2OKL; Ligand: BB2; Similar sites found: 117
This union binding pocket(no: 1) in the query (biounit: 2okl.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KO0 TFP 0.0023 0.46322 None
2 1UO5 PIH 0.01447 0.43496 None
3 4GK9 MAN BMA MAN MAN MAN 0.005961 0.42498 None
4 5EXA 5SO 0.01203 0.41036 None
5 2ALG HP6 0.00835 0.40383 None
6 2ALG DAO 0.00835 0.40383 None
7 1KUK PCA LYS TRP 0.00001047 0.49959 1.08108
8 3WYJ H78 0.03789 0.40935 2.16216
9 1A8P FAD 0.00869 0.4013 2.16216
10 3Q2H QHF 0.00002163 0.50053 2.7027
11 3B9Z CO2 0.001769 0.46984 2.7027
12 4RW3 TDA 0.005615 0.42833 2.7027
13 2YB9 HA0 0.01823 0.42606 2.7027
14 3U4C NDP 0.005205 0.42383 2.7027
15 3G58 988 0.006795 0.41803 2.7027
16 1XMU ROF 0.006168 0.4116 2.7027
17 1XON PIL 0.009726 0.41132 2.7027
18 1XMY ROL 0.01165 0.41105 2.7027
19 1XM4 PIL 0.0103 0.40525 2.7027
20 2AMV BIN 0.03472 0.40411 2.7027
21 1RM8 BAT 0.00004489 0.44784 2.95858
22 5V4R MGT 0.0006478 0.49015 3.08642
23 1ATL 0QI 0.00002619 0.51733 3.24324
24 4MGA 27L 0.01198 0.42347 3.24324
25 4QOM PYG 0.00379 0.41725 3.24324
26 2A1L PCW 0.0186 0.41185 3.24324
27 4QHP 32Q 0.005907 0.41053 3.24324
28 1T27 PCW 0.02328 0.40625 3.24324
29 4KWD JF2 0.009736 0.40568 3.24324
30 1NF8 BOG 0.02355 0.40486 3.24324
31 4K90 MLA 0.02295 0.40118 3.24324
32 1JGS SAL 0.001646 0.41028 3.62319
33 4NAT ADP 0.04799 0.41185 3.75
34 4AIG FLX 0.00001293 0.5484 3.78378
35 2OUA AES 0.009192 0.43169 3.78378
36 2V57 PRL 0.006618 0.43113 3.78378
37 3C88 ARG ARG GLY CYS NH2 0.03022 0.40407 3.78378
38 3H0A D30 0.01238 0.4038 3.78378
39 3HBV ALA LYS ALA SER GLN ALA ALA 0.00282 0.40257 3.78378
40 4Q5M ROC 0.01871 0.40061 3.78378
41 3R1V AZB 0.006614 0.41328 3.93701
42 3KP6 SAL 0.0005819 0.48788 3.97351
43 2J83 BAT 0.00002764 0.51159 4.32432
44 4ARF IP8 GLY PRO ALA 0.0003943 0.44864 4.32432
45 2NAD NAD 0.009989 0.41793 4.32432
46 1UI0 URA 0.01605 0.41545 4.32432
47 3NFD COA 0.005502 0.42712 4.57516
48 1Q3A NGH 0.000006901 0.48702 4.84848
49 4DV8 0LX 0.0003359 0.48587 4.86486
50 1BKC INN 0.00001985 0.4854 4.86486
51 1FBL HTA 0.0000213 0.47704 4.86486
52 2FV5 541 0.000006966 0.43808 4.86486
53 4V3I ASP LEU THR ARG PRO 0.008387 0.43095 4.86486
54 4AR8 IP8 GLY PRO ALA 0.001102 0.43019 4.86486
55 3GKJ HC3 0.005674 0.4095 4.86486
56 3SP6 IL2 0.005557 0.40801 4.86486
57 3AHO 3A2 0.0121 0.4014 4.86486
58 5UC9 MYR 0.01801 0.40168 4.86726
59 1HFS L04 0.001034 0.46038 5
60 5IF4 6AK 0.01667 0.40846 5.03145
61 1U4J MAN 0.02693 0.40028 5.08475
62 1N13 AG2 0.01628 0.41114 5.30973
63 2TCL RO4 0.000196 0.47405 5.32544
64 2ZXG S23 0.0009038 0.45401 5.40541
65 3TDC 0EU 0.01602 0.44285 5.40541
66 5EW9 5VC 0.04545 0.41907 5.40541
67 2ZCQ B65 0.02331 0.4071 5.40541
68 3V1S 0LH 0.02591 0.40526 5.40541
69 2V5E SCR 0.00358 0.45738 5.94059
70 4WKI 3PW 0.000005401 0.55862 5.94595
71 1YP1 LYS ASN LEU 0.00000368 0.48117 5.94595
72 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.002656 0.46706 5.94595
73 2Z9I GLY ALA THR VAL 0.003853 0.45199 5.94595
74 4GAA BES 0.0007135 0.44953 5.94595
75 4ZOM 4Q3 0.01632 0.40991 5.94595
76 2VCX GSH 0.04324 0.40006 5.94595
77 2VCX D26 0.04324 0.40006 5.94595
78 1IDA 0PO 0.01891 0.40482 6.06061
79 1R55 097 0.00001213 0.47522 6.48649
80 5IKH 6BW 0.01361 0.40823 6.48649
81 4WZV E40 0.0002517 0.47735 6.875
82 1VPD TLA 0.006313 0.43334 7.02703
83 4DFU QUE 0.02257 0.40101 7.45342
84 3KA2 2NC 0.03736 0.4018 7.56757
85 1MMQ RRS 0.0001865 0.47031 7.64706
86 1BWO LPC 0.007755 0.40164 7.77778
87 1ZVX FIN 0.0004194 0.48136 7.97546
88 4KX8 L2O VAL VAL ASP 0.000865 0.44559 8.10811
89 3R9V DXC 0.01056 0.42073 8.10811
90 5L2J 6UL 0.03636 0.41026 8.10811
91 5IR4 ZPE 0.02301 0.40649 8.10811
92 3WV1 WHH 0.0008043 0.47642 8.18713
93 3HY9 098 0.000005497 0.53984 8.64865
94 4DD8 BAT 0.000008007 0.46897 8.64865
95 3AQT RCO 0.004018 0.44482 8.64865
96 4UCC ZKW 0.01505 0.4181 9.18919
97 4F4S EFO 0.01682 0.40752 9.21053
98 5OCA 9QZ 0.00788 0.43842 9.52381
99 2VWA PTY 0.005144 0.44212 9.90099
100 3ZVS MLI 0.0004993 0.42031 10
101 4LBP 1WG 0.01404 0.40704 10
102 4B6C B5U 0.006449 0.40686 10.2703
103 1RTW MP5 0.02357 0.40004 10.2703
104 3GXO MQA 0.01871 0.40086 10.8108
105 4ZW3 4S9 0.0003477 0.48517 13.5135
106 2W14 WR2 0.0001042 0.46523 13.5135
107 2QZT PLM 0.004766 0.42419 13.5135
108 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.01175 0.41003 14.0541
109 3T3C 017 0.008018 0.41384 14.1414
110 3DLG GWE 0.03264 0.41144 15.1351
111 5T2Z 017 0.01421 0.40372 15.1515
112 3WCA FPS 0.004954 0.42481 15.6757
113 5CSD ACD 0.02575 0.4014 16.3522
114 3W68 VIV 0.007436 0.40778 25.4054
115 2Y69 CHD 0.01056 0.41906 36.5079
116 1G27 BB1 0.000000000006372 0.77257 42.2619
117 1RL4 BRR 0.0000000003141 0.79782 47.027
Pocket No.: 2; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2okl.bio2) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found: 11
This union binding pocket(no: 3) in the query (biounit: 2okl.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RJD TFP 0.02457 0.40126 None
2 4J7U NAP 0.02564 0.40508 2.7027
3 4J7U YTZ 0.02564 0.40508 2.7027
4 4DS0 A2G GAL NAG FUC 0.01145 0.40264 3.06748
5 2HW1 FRU 0.02323 0.40238 3.78378
6 2O4N TPV 0.0138 0.40025 7.07071
7 1FIQ FAD 0.009395 0.41808 8.6758
8 4GDX GLU 0.02593 0.4024 10.8108
9 4ZBY URA 0.03084 0.40038 10.8108
10 3RLF MAL 0.01861 0.40097 12.973
11 2DYR PGV 0.01973 0.40498 21.4286
Pocket No.: 4; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2okl.bio1) has 5 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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