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 250 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 217 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 181 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: 36
This union binding pocket(no: 1) in the query (biounit: 4s00.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VRQ XYP XYP AHR 0.01032 0.4163 1.566
2 4H8N NDP 0.02646 0.41137 1.6129
3 1ZAP A70 0.005076 0.45208 1.75439
4 4QWT ACD 0.03015 0.40422 1.78971
5 3EWC MCF 0.03297 0.40015 1.88679
6 5BX3 NOJ 0.02034 0.40142 2.23714
7 1S1D GP2 0.006313 0.43157 2.41692
8 2PCU ASP 0.00735 0.41664 2.62295
9 3FV3 IVA VAL VAL STA ALA STA 0.01384 0.42498 2.65487
10 1WKM MET 0.0002913 0.47806 2.71186
11 3AGC RCC 0.01492 0.41867 3.62319
12 2BO9 VAL 0.00848 0.41063 4.05405
13 3QP8 HL0 0.02125 0.4015 4.34783
14 2QZX IVA VAL VAL STA ALA STA 0.008013 0.43321 4.38596
15 1T27 PCW 0.03286 0.41609 4.42804
16 3RYC GTP 0.03099 0.40807 4.94382
17 1U0A BGC BGC BGC BGC 0.01661 0.40444 5.14019
18 5EYP GDP 0.03367 0.4046 5.32544
19 1X1Z BMP 0.03019 0.4224 5.95238
20 2OAZ I96 0.0285 0.40238 5.96206
21 3VNM SDD 0.009793 0.4219 6.82594
22 5A65 TPP 0.01428 0.41925 6.91244
23 4WUJ FMN 0.01919 0.40755 7.48299
24 5ITZ GDP 0.02281 0.4091 11.6279
25 5M4Q PRO 0.001616 0.41245 12.528
26 5JNN 6LM 0.02775 0.40092 12.6316
27 3UP3 XCA 0.03075 0.4037 14.4033
28 4ZWP M44 0.00277 0.41242 15.9091
29 1QXW M1C 0.0004461 0.49208 16.6667
30 3TMK T5A 0.02702 0.41086 16.6667
31 2IBZ SMA 0.03051 0.40213 17.5676
32 4NG2 OHN 0.01806 0.41319 18.5841
33 1QFT HSM 0.0153 0.40362 20
34 4IKR PVP 0.0005141 0.50588 20.6687
35 3IU9 T07 0.04491 0.44886 32.9861
36 1YVM TMG 0.0004514 0.48443 36.7424
Pocket No.: 2; Query (leader) PDB : 4S00; Ligand: AKR; 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: 4s00.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4S00; Ligand: AKR; Similar sites found: 27
This union binding pocket(no: 3) in the query (biounit: 4s00.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZKJ ADP 0.04114 0.40845 1.77665
2 4V24 GYR 0.03106 0.4026 1.88679
3 3A7R LAQ 0.0449 0.40296 2.37389
4 5F2K OCA 0.03394 0.41024 2.44565
5 5F2K SAH 0.03394 0.41024 2.44565
6 2ZB4 NAP 0.04978 0.40898 2.52101
7 3A06 FOM 0.03592 0.4093 2.65957
8 3RFA SAM 0.01305 0.41055 2.90828
9 4O8O AHR 0.005686 0.4283 3.80313
10 5GQF GAL NAG 0.009659 0.41271 3.80313
11 3EBL GA4 0.02367 0.40527 3.83562
12 1RO7 CSF 0.02931 0.40533 3.861
13 2DW7 SRT 0.01153 0.40994 4.11311
14 1Y0G 8PP 0.0314 0.40755 4.18848
15 3V4S ADP 0.04471 0.40662 4.39277
16 1I06 TZL 0.006766 0.40832 4.44444
17 2IV2 2MD 0.04386 0.40237 4.47427
18 3WN0 FUB 0.02114 0.40545 4.79452
19 1QZY TDE 0.01529 0.41019 4.9217
20 4N2R FUB 0.01026 0.40628 5.68862
21 2Z93 END 0.01063 0.41003 6.57277
22 2WVZ KIF 0.0122 0.41622 6.71141
23 2P7Q GG6 0.01431 0.40032 6.76692
24 4CVC PQQ 0.0124 0.40773 7.15884
25 2D3S TNR 0.01604 0.40635 7.85124
26 5JE0 AZ8 0.04144 0.40096 8.09717
27 5JE0 SAH 0.04144 0.40096 8.09717
Pocket No.: 4; Query (leader) PDB : 4S00; Ligand: AKR; 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: 4s00.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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