Receptor
PDB id Resolution Class Description Source Keywords
1BS8 2.2 Å EC: 3.5.1.31 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER ESCHERICHIA COLI HYDROLASE IRON METALLOPROTEASE; PROTEIN SYNTHESIS
Ref.: IRON CENTER, SUBSTRATE RECOGNITION AND MECHANISM OF PEPTIDE DEFORMYLASE. NAT.STRUCT.BIOL. V. 5 1053 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MET ALA SER D:1;
E:1;
F:1;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
291.348 n/a S(CCC...
SO4 B:3001;
B:3002;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:2001;
B:2001;
C:2001;
Part of Protein;
Part of Protein;
Part of Protein;
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
1G27 2.1 Å EC: 3.5.1.31 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH THE INHIBITOR BB-3497 ESCHERICHIA COLI BB-3497 INHIBITION POLYPEPTIDE DEFORMYLASE HYDROLASE
Ref.: ANTIBIOTIC ACTIVITY AND CHARACTERIZATION OF BB-3497, A NOVEL PEPTIDE DEFORMYLASE INHIBITOR. ANTIMICROB.AGENTS CHEMOTHER. V. 45 563 2001
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
7 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
8 1IX1 - 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: MET ALA SER; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 MET ALA SER 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1G27; Ligand: BB1; Similar sites found: 99
This union binding pocket(no: 1) in the query (biounit: 1g27.bio3) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RM8 BAT 0.00002296 0.44605 None
2 3NFD COA 0.006994 0.42394 None
3 1BWO LPC 0.004381 0.40891 None
4 5K53 STE 0.00535 0.40707 None
5 4RC8 STE 0.006543 0.40679 None
6 4B6C B5U 0.006456 0.40167 None
7 3ZVS MLI 0.000976 0.40005 1.25
8 4WKI 3PW 0.00001653 0.47921 1.2766
9 4AIG FLX 0.00003575 0.45942 1.78571
10 3W68 VIV 0.00455 0.4137 1.78571
11 4OIV XX9 0.01648 0.4076 1.78571
12 3OKI OKI 0.02433 0.40058 1.78571
13 2FP2 TSA 0.0065 0.40154 1.80723
14 2ED4 FAD 0.009787 0.40655 2.01342
15 1KAP GLY SER ASN SER 0.0003977 0.42456 2.97619
16 5BSR COA 0.0165 0.42061 2.97619
17 5BSR AMP 0.0132 0.41496 2.97619
18 2W14 WR2 0.00003458 0.47598 3.57143
19 4BXK 1IU 0.001407 0.45509 3.57143
20 4ARF IP8 GLY PRO ALA 0.0006644 0.43048 3.57143
21 4PJT 2YQ 0.01415 0.40189 3.57143
22 3WV1 WHH 0.0001077 0.51306 4.16667
23 4ZW3 4S9 0.0001783 0.49379 4.16667
24 4AR8 IP8 GLY PRO ALA 0.00009897 0.46442 4.16667
25 3WYJ H78 0.01481 0.42685 4.16667
26 4PGK Y69 0.008948 0.421 4.16667
27 3COW 52H 0.0266 0.40308 4.16667
28 2AX9 BHM 0.008019 0.42323 4.7619
29 3EE4 MYR 0.006314 0.40575 4.7619
30 1NAA 6FA 0.02469 0.40463 4.7619
31 5X40 ACP 0.008858 0.40102 4.7619
32 4GQL R47 0.00006504 0.51676 5.03145
33 4QOM PYG 0.003599 0.41452 5.35714
34 2XQ0 BES 0.0007071 0.40244 5.35714
35 3X1M COA 0.02565 0.41623 5.66038
36 3Q2H QHF 0.00001214 0.5187 5.95238
37 4CA5 3EF 0.0009318 0.47604 5.95238
38 2IV2 MGD 0.006594 0.42406 5.95238
39 1HN4 MJI 0.04211 0.40488 6.10687
40 2QZT PLM 0.00813 0.41017 6.30631
41 1ATL 0QI 0.000008923 0.53202 6.54762
42 2TCL RO4 0.00001948 0.51243 6.54762
43 1MMQ RRS 0.00001205 0.51028 6.54762
44 2VJ8 HA2 0.000735 0.47169 6.54762
45 1FBL HTA 0.00002303 0.46579 6.54762
46 1R5L VIV 0.004259 0.41827 6.54762
47 4B52 RDF 0.001733 0.40858 6.54762
48 2C78 PUL 0.03832 0.40199 6.54762
49 4WZV E40 0.00002874 0.51414 6.875
50 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.0003766 0.47753 7.14286
51 3C88 ARG ARG GLY CYS NH2 0.01003 0.42416 7.14286
52 5AAV GW5 0.02065 0.41446 7.14286
53 1Q3A NGH 0.000001927 0.49406 7.27273
54 2ZXG S23 0.0001548 0.48372 7.7381
55 2J83 BAT 0.0001006 0.48165 7.7381
56 3DBK RDF 0.00297 0.41617 7.7381
57 5C2H 4XU 0.01666 0.40104 7.7381
58 1HFS L04 0.00004573 0.51779 8.125
59 3HY9 098 0.00001573 0.51387 8.33333
60 2E2R 2OH 0.01526 0.40503 8.33333
61 1ZVX FIN 0.00005157 0.5185 8.58896
62 4KX8 L2O VAL VAL ASP 0.0002474 0.46477 8.92857
63 3HBV ALA LYS ALA SER GLN ALA ALA 0.00009449 0.44966 8.92857
64 4RFM 3P6 0.01818 0.41182 8.92857
65 2R4J 13P 0.02613 0.40877 8.92857
66 2R4J FAD 0.02613 0.40877 8.92857
67 1YP1 LYS ASN LEU 0.00000391 0.47027 9.52381
68 4GAA BES 0.0003871 0.44083 9.52381
69 3AHO 3A2 0.003462 0.42225 9.52381
70 5G5G MCN 0.008331 0.41936 9.52381
71 1G8K MGD 0.04643 0.40496 9.52381
72 3DLG GWE 0.04796 0.40029 9.52381
73 4DV8 0LX 0.0001509 0.49712 10.7143
74 4QHP 32Q 0.0007344 0.44639 10.7143
75 4AG8 AXI 0.01844 0.40123 10.7143
76 1KUK PCA LYS TRP 0.000009468 0.48979 11.3095
77 4DD8 BAT 0.00002399 0.44795 11.3095
78 4TMN 0PK 0.00447 0.41572 11.3095
79 2ZCQ B65 0.02112 0.40618 11.3095
80 4IGH 1EA 0.03102 0.41152 11.9048
81 4IGH FMN 0.03102 0.41152 11.9048
82 4IGH ORO 0.03102 0.41152 11.9048
83 1UUO BRF 0.03165 0.40674 11.9048
84 3KV8 FAH 0.04228 0.4018 12.2302
85 2YB9 HA0 0.01144 0.43304 13.6905
86 1XVB BHL 0.01641 0.40768 13.6905
87 2FV5 541 0.000006626 0.55238 16.6667
88 1BKC INN 0.00001153 0.48621 16.6667
89 2V3V MGD 0.04028 0.40966 16.6667
90 3H0A D30 0.01236 0.40064 17.2619
91 1OUK 084 0.03597 0.42172 19.0476
92 1R55 097 0.00006737 0.44208 20.2381
93 3SVJ 4LI 0.00000000007816 0.74929 38.0952
94 5JF2 SF7 0.000000001031 0.69341 38.0952
95 1Q1Y BB2 0.00000000004631 0.7055 38.6905
96 3G6N MET ALA SER 0.000000007067 0.57075 38.6905
97 2OKL BB2 0.000000000006372 0.77257 42.2619
98 1LQY BB2 0.000000000001097 0.8048 47.619
99 3G5K BB2 0.00000000002061 0.73483 47.619
Pocket No.: 2; Query (leader) PDB : 1G27; Ligand: BB1; Similar sites found: 29
This union binding pocket(no: 2) in the query (biounit: 1g27.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VCX D26 0.04249 0.40044 1.78571
2 2VCX GSH 0.04249 0.40044 1.78571
3 1M5B BN1 0.03866 0.42437 3.57143
4 4ZOM 4Q3 0.02301 0.40278 3.57143
5 5K52 OCD 0.01007 0.40021 3.57143
6 5LGA 6VH 0.01793 0.40485 4.16667
7 1EJ4 M7G 0.02705 0.40276 4.16667
8 5CSD ACD 0.0236 0.40126 5.03145
9 3KDU NKS 0.008267 0.42395 5.35714
10 3KFC 61X 0.01711 0.40358 5.35714
11 2OBD PCW 0.01652 0.40192 5.35714
12 4ORM ORO 0.01643 0.42773 5.95238
13 4ORM 2V6 0.01643 0.42773 5.95238
14 4ORM FMN 0.01643 0.42773 5.95238
15 3G4G D71 0.005487 0.40825 6.54762
16 3G58 988 0.006345 0.40351 6.54762
17 3KPB SAM 0.0158 0.40634 6.55738
18 3TGE TGE 0.0426 0.40107 7.14286
19 5HI5 63Q 0.01272 0.40462 8.33333
20 3LN0 52B 0.03426 0.40367 8.92857
21 1N4W FAD 0.01565 0.41635 9.52381
22 4NAT ADP 0.04622 0.4127 10
23 4JNA FAD 0.03235 0.40017 11.9048
24 5FVJ ACO 0.0118 0.40477 12.6506
25 4IN9 SER TRP PHE PRO 0.0002222 0.40153 13.253
26 1TT8 PHB 0.01217 0.40275 13.4146
27 2VQD AP2 0.006261 0.40761 13.6905
28 3FUR Z12 0.03429 0.40058 17.2619
29 3DST GRG 0.04613 0.40984 20.2381
Pocket No.: 3; Query (leader) PDB : 1G27; Ligand: BB1; Similar sites found: 14
This union binding pocket(no: 3) in the query (biounit: 1g27.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CZG ADP 0.01448 0.40609 3.57143
2 4P6G 2FZ 0.01513 0.40179 3.57143
3 2I0D MUT 0.04915 0.40093 4.0404
4 3GZ9 D32 0.007853 0.42264 4.16667
5 1AOE NDP 0.02224 0.40243 4.16667
6 1AOE GW3 0.02224 0.40243 4.16667
7 1B7H LYS NLE LYS 0.01702 0.40174 4.16667
8 3KRR DQX 0.04523 0.40157 5.35714
9 5BVE 4VG 0.03968 0.40317 6.54762
10 4YDD MGD 0.04616 0.40665 8.92857
11 4YDD MD1 0.04616 0.40665 8.92857
12 3AB1 FAD 0.02073 0.40478 11.3095
13 1UUO FMN 0.02739 0.40847 11.9048
14 1UUO ORO 0.02739 0.40847 11.9048
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