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Receptor
PDB id Resolution Class Description Source Keywords
4S00 2.1 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF METALLOPEPTIDASE-LIKE DIMETHYLSULPHONIO (DMSP) LYASE RLDDDP MUTANT Y366A IN COMPLEX WITH ACRYLATE SILICIBACTER LACUSCAERULENSIS ITI-1157ORGANISM_TAXID: 644107 METALLOPEPTIDASE-LIKE DMSP LYASE LYASE
Ref.: STRUCTURAL AND MOLECULAR BASIS FOR THE NOVEL CATALY MECHANISM AND EVOLUTION OF DDDP, AN ABUNDANT PEPTID BACTERIAL DIMETHYLSULFONIOPROPIONATE LYASE: A NEW E FROM AN OLD FOLD. MOL.MICROBIOL. V. 98 289 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE C:502;
D:501;
A:501;
C:501;
D:502;
A:502;
B:502;
B:501;
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;
submit data
55.845 Fe [Fe+3...
GOL D:504;
D:503;
C:504;
A:504;
A:505;
D:505;
C:505;
B:505;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
AKR B:503;
A:503;
C:503;
B:504;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
72.063 C3 H4 O2 C=CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4S00 2.1 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF METALLOPEPTIDASE-LIKE DIMETHYLSULPHONIO (DMSP) LYASE RLDDDP MUTANT Y366A IN COMPLEX WITH ACRYLATE SILICIBACTER LACUSCAERULENSIS ITI-1157ORGANISM_TAXID: 644107 METALLOPEPTIDASE-LIKE DMSP LYASE LYASE
Ref.: STRUCTURAL AND MOLECULAR BASIS FOR THE NOVEL CATALY MECHANISM AND EVOLUTION OF DDDP, AN ABUNDANT PEPTID BACTERIAL DIMETHYLSULFONIOPROPIONATE LYASE: A NEW E FROM AN OLD FOLD. MOL.MICROBIOL. V. 98 289 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 4S00 - AKR C3 H4 O2 C=CC(=O)O
2 4S01 - AKR C3 H4 O2 C=CC(=O)O
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 4S00 - AKR C3 H4 O2 C=CC(=O)O
2 4S01 - AKR C3 H4 O2 C=CC(=O)O
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 4S00 - AKR C3 H4 O2 C=CC(=O)O
2 4S01 - AKR C3 H4 O2 C=CC(=O)O
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 AKR 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4S00; Ligand: AKR; Similar sites found with APoc: 94
This union binding pocket(no: 1) in the query (biounit: 4s00.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2VFT SOR 1.65877
2 5K8B PDG 1.73697
3 1ZAP A70 1.75439
4 4QWT ACD 1.78971
5 3WUG XYP 1.91693
6 3DRG ARG PRO PRO GLY PHE SER PRO PHE ALA 2.01342
7 6AM8 PLT 2.01342
8 4K26 SFF 2.01342
9 5Y72 DST 2.08955
10 5HSS 64Z 2.15633
11 3Q60 ATP 2.15633
12 5HSS 650 2.15633
13 5YBN AKG 2.2293
14 5BX3 NOJ 2.23714
15 5HZX 2GE 2.27273
16 3D9F FAD 2.28311
17 3D9F N6C 2.28311
18 1S1D GP2 2.41692
19 5F2K OCA 2.44565
20 5F2K SAH 2.44565
21 2PCU ASP 2.62295
22 3A06 FOM 2.65957
23 1WKM MET 2.71186
24 4OYA 1VE 2.90828
25 3ETG GLU 2.90828
26 3ETG NDP 2.90828
27 1GNI OLA 3.13199
28 4X17 SIA SIA 3.30882
29 5UR6 8KM 3.31492
30 6GBX S77 3.34347
31 4NV7 COA 3.84615
32 6F4W FMC 3.86266
33 1V8B ADN 4.02685
34 5GM5 CBI 4.09091
35 2DW7 SRT 4.11311
36 5ZM4 9FU 4.24837
37 3QP8 HL0 4.34783
38 2GWH PCI 4.36242
39 2AMT GPP 4.40252
40 5MN0 A8S 4.78469
41 2WA4 069 4.87106
42 1QZY TDE 4.9217
43 4LNU GDP 4.94382
44 1U0A BGC BGC BGC BGC 5.14019
45 3O75 F1X 5.14706
46 3H7J PPY 5.34979
47 4IPE ANP 5.36913
48 1DTL BEP 5.59006
49 5BU3 4W9 5.97826
50 1MDC PLM 6.06061
51 1DE6 RNS 6.10329
52 2YOH WMJ 6.19048
53 3N8K D1X 6.39535
54 3H22 B53 6.39731
55 1NNU TCT 6.55022
56 1NNU NAD 6.55022
57 2Z93 END 6.57277
58 2P7Q GG6 6.76692
59 3VNM SDD 6.82594
60 5A65 TPP 6.91244
61 4CVC PQQ 7.15884
62 5VSM 5AD 7.2327
63 5VSM MET 7.2327
64 4WUJ FMN 7.48299
65 2D3S TNR 7.85124
66 5JE0 SAH 8.09717
67 5JE0 AZ8 8.09717
68 5TBM 79A 8.69565
69 6CLV 6MB 8.72483
70 5CSD ACD 8.80503
71 6E08 NAP 8.94855
72 4CPB GAL CN8 9.09091
73 4CP9 GAL CN8 9.09091
74 2V54 TYD 9.80392
75 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 11.1111
76 5M4Q PRO 12.528
77 3HPY MCT 13.5922
78 3KDJ A8S 13.8614
79 3UP3 XCA 14.4033
80 1EYE PMM 15
81 1AJ0 SAN 15.2482
82 1AJ0 PH2 15.2482
83 3L24 GOA 15.8837
84 4ZWP M44 15.9091
85 3TMK T5A 16.6667
86 4NG2 OHN 18.5841
87 1QFT HSM 20
88 4IKR PVP 20.6687
89 5EIB GTP 21.7391
90 2DYR PGV 30.4348
91 5ZCO PGV 30.4348
92 1M3U KPL 31.0606
93 3IU9 T07 32.9861
94 1YVM TMG 36.7424
Pocket No.: 2; Query (leader) PDB : 4S00; Ligand: AKR; Similar sites found with APoc: 52
This union binding pocket(no: 2) in the query (biounit: 4s00.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2WYA HMG 1.78971
2 4V24 GYR 1.88679
3 5I49 2KH 2.23714
4 4DOL PLM 2.30415
5 6CUZ FEV 2.31959
6 2RDT FMN 2.32558
7 3UG4 AHR 2.46085
8 4XDA ADP 2.589
9 3ZXR P3S 2.68456
10 3ZXR IQ1 2.68456
11 6GNF QPS 2.68456
12 3MA0 XYP 2.8754
13 3ETG GTP 2.90828
14 3WH1 NAG NAG NAG NAG 2.91262
15 4H9T HL4 3.0303
16 3HBN UDP 3.19149
17 4YWA 4J9 3.30579
18 4X17 SIA 3.30882
19 5NEA 8V8 3.46154
20 4JK3 NAD 3.4749
21 2OGA PGU 3.50877
22 1N7G GDR 3.67454
23 5GQF GAL NAG 3.80313
24 5XWC 8GL 3.80313
25 5XWC NAP 3.80313
26 5XWC 2IT 3.80313
27 1KJ8 ATP 3.83632
28 4CNO 9PY 3.96825
29 4CLI 5P8 3.97554
30 3PIJ FRU 4.02685
31 1YNH SUO 4.25056
32 1T27 PCW 4.42804
33 6FOG OXL 4.46429
34 5GUD 2IT 4.47427
35 5GUD NDP 4.47427
36 3T50 FMN 4.6875
37 2DSA GSH 4.92611
38 2DSA HPX 4.92611
39 6GG9 FMN 4.93827
40 2CJF RP4 5.09554
41 5SVV FMN 5.10949
42 4POJ 2VP 5.19481
43 2VPQ ANP 5.36913
44 2V0U FMN 6.16438
45 3VZS CAA 6.61479
46 2OBD 2OB 7.60626
47 2AGC DAO 9.87654
48 1EOM NAG MAN MAN MAN NAG GAL NAG GAL 10
49 6AP8 BNY 10.0372
50 2QO4 CHD 11.1111
51 6CED EYA 12.1495
52 3VPB ADP 12.5
Pocket No.: 3; Query (leader) PDB : 4S00; Ligand: AKR; Similar sites found with APoc: 24
This union binding pocket(no: 3) in the query (biounit: 4s00.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 2PP3 LGT 1.50754
2 2VOT NHV 1.78971
3 3A06 NDP 2.65957
4 4ZAC 4LU 2.68456
5 3RFA SAM 2.90828
6 5HIP 61O 2.9703
7 4UDB CV7 3.67647
8 5VZ0 ADP 3.80313
9 1HG4 LPP 3.94265
10 2H6T IVA VAL VAL STA ALA STA 4.11765
11 1Y0G 8PP 4.18848
12 4JAW NGT GAL 4.25056
13 6F1J EDG 4.30769
14 2A1L PCW 5.18518
15 2BES RES 5.23256
16 1VL8 NAP 5.24345
17 3EM0 CHD 6.52174
18 4M44 SIA GAL NAG GAL 6.59341
19 5LXT ACP 8.07292
20 2FR6 CTN 8.90411
21 4LA7 A1O 12.4352
22 1QIN GIP 12.5683
23 3F10 8HG 15.7534
24 1QXW M1C 16.6667
Pocket No.: 4; Query (leader) PDB : 4S00; Ligand: AKR; Similar sites found with APoc: 13
This union binding pocket(no: 4) in the query (biounit: 4s00.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2VRQ XYP XYP AHR 1.566
2 3ERR AMP 2.01342
3 1W2T SUC GLA 2.08333
4 1GT6 OLA 2.60223
5 3FV3 IVA VAL VAL STA ALA STA 2.65487
6 2XB8 XNW 3.42466
7 5DKK FMN 3.44828
8 4PB2 5UD 3.53774
9 2QZX IVA VAL VAL STA ALA STA 4.38596
10 5COU ATP 5.29412
11 4L9P FII 5.72207
12 3UA1 08Y 6.04027
13 5Z84 PGV 30.4348
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