Receptor
PDB id Resolution Class Description Source Keywords
2VD9 2.1 Å EC: 5.1.1.1 THE CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252) WITH BOUND L-ALA-P BACILLUS ANTHRACIS PYRIDOXAL 5-prime -PHOSPHATE PEPTIDOGLYCAN SYNTHESIS PLP OPPF L-ALANINE ISOMERASE D-ALANINE PYRIDOXAL PHOSPHATE STRUCTURAL GENOMICS ALANINE RACEMASE SPORE GERMINATION OXFORD PROTEIN PRODUCTION FACILITY STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
Ref.: STRUCTURES OF AN ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252) IN THE PRESENCE AND ABSENCE OF (R)-1-AMINOETHYLPHOSPHONIC ACID (L-ALA-P). ACTA CRYSTALLOGR.,SECT.F V. 64 327 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:1392;
A:1393;
B:1391;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
EPC A:1395;
B:1393;
Valid;
Valid;
none;
none;
submit data
354.19 C10 H16 N2 O8 P2 Cc1c(...
IN5 A:1394;
B:1392;
Valid;
Valid;
none;
none;
submit data
356.206 C10 H18 N2 O8 P2 Cc1c(...
MG A:1390;
A:1391;
B:1390;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VD9 2.1 Å EC: 5.1.1.1 THE CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252) WITH BOUND L-ALA-P BACILLUS ANTHRACIS PYRIDOXAL 5-prime -PHOSPHATE PEPTIDOGLYCAN SYNTHESIS PLP OPPF L-ALANINE ISOMERASE D-ALANINE PYRIDOXAL PHOSPHATE STRUCTURAL GENOMICS ALANINE RACEMASE SPORE GERMINATION OXFORD PROTEIN PRODUCTION FACILITY STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
Ref.: STRUCTURES OF AN ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252) IN THE PRESENCE AND ABSENCE OF (R)-1-AMINOETHYLPHOSPHONIC ACID (L-ALA-P). ACTA CRYSTALLOGR.,SECT.F V. 64 327 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2VD9 - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 2VD9 - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1BD0 - IN5 C10 H18 N2 O8 P2 Cc1c(c(c(c....
2 1XQK - PMH C11 H14 N3 O7 P Cc1c(c(c(c....
3 1XQL - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1FTX - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
5 2SFP Ki = 20 mM PPI C3 H6 O2 CCC(=O)O
6 1L6G - PDD C11 H17 N2 O7 P Cc1c(c(c(c....
7 1NIU Ki = 0.08 uM DCS C11 H16 N3 O7 P Cc1c(c(c(c....
8 1L6F - PP3 C11 H17 N2 O7 P Cc1c(c(c(c....
9 2VD9 - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
10 3E5P - PPI C3 H6 O2 CCC(=O)O
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EPC; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 EPC 1 1
2 KOU 0.676923 0.857143
3 6DF 0.661765 0.941176
4 PL6 0.637681 0.872727
5 EXT 0.615385 0.888889
6 PL5 0.608108 0.827586
7 PLP 0.603448 0.862745
8 0JO 0.597015 0.857143
9 4LM 0.597015 0.907407
10 PZP 0.59322 0.901961
11 MPM 0.588235 0.942308
12 PUS 0.586667 0.727273
13 5DK 0.584416 0.774194
14 HCP 0.571429 0.857143
15 P3D 0.571429 0.783333
16 Z98 0.561644 0.8
17 PLT 0.554217 0.813559
18 AN7 0.529412 0.830189
19 LLP 0.525641 0.786885
20 FOO 0.5 0.87037
21 P89 0.493827 0.790323
22 PLP PUT 0.493333 0.767857
23 PLP PHE 0.481928 0.785714
24 O1G 0.481928 0.8
25 PLR 0.47541 0.88
26 PFM 0.461538 0.793103
27 P0P 0.461538 0.826923
28 PLP ABU 0.461538 0.758621
29 IN5 0.458333 0.810345
30 PLP MYB 0.453488 0.686567
31 PXP 0.446154 0.781818
32 PLP PVH 0.443182 0.734375
33 PMP 0.439394 0.789474
34 GT1 0.432836 0.785714
35 PDA 0.421053 0.783333
36 PDD 0.421053 0.783333
37 PP3 0.421053 0.783333
38 PLS 0.410256 0.741935
39 TLP 0.410256 0.783333
40 2BO 0.410256 0.783333
41 2BK 0.410256 0.783333
42 C6P 0.405063 0.741935
Ligand no: 2; Ligand: IN5; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 IN5 1 1
2 PDA 0.703125 0.965517
3 PDD 0.703125 0.965517
4 PP3 0.703125 0.965517
5 2BK 0.681818 0.932203
6 TLP 0.681818 0.932203
7 2BO 0.681818 0.932203
8 C6P 0.671642 0.885246
9 PLS 0.656716 0.885246
10 PPD 0.647059 0.885246
11 ILP 0.642857 0.901639
12 PY5 0.637681 0.859375
13 PLG 0.630769 0.885246
14 PGU 0.619718 0.857143
15 PDG 0.619718 0.857143
16 7XF 0.619718 0.857143
17 33P 0.617647 0.915254
18 QLP 0.611111 0.80597
19 P1T 0.602941 0.84375
20 76U 0.60274 0.815385
21 PY6 0.60274 0.861538
22 N5F 0.594595 0.84375
23 ORX 0.594595 0.84375
24 PE1 0.586667 0.84375
25 5PA 0.585714 0.84375
26 PXP 0.583333 0.842105
27 KAM 0.576923 0.873016
28 PMP 0.57377 0.912281
29 IK2 0.571429 0.815385
30 PL4 0.571429 0.84375
31 GT1 0.564516 0.783333
32 PMH 0.56338 0.736111
33 CBA 0.554054 0.857143
34 PLA 0.547945 0.888889
35 DCS 0.546667 0.72973
36 PLP ALO 0.541667 0.883333
37 7TS 0.533333 0.72
38 EA5 0.532468 0.818182
39 AQ3 0.53012 0.830769
40 PMG 0.526316 0.861538
41 PL2 0.526316 0.776119
42 HEY 0.519481 0.830769
43 3LM 0.512821 0.833333
44 PSZ 0.512821 0.791045
45 9YM 0.506329 0.828125
46 PXG 0.493827 0.854839
47 RW2 0.493827 0.791045
48 PL8 0.487805 0.75
49 7B9 0.47619 0.782609
50 PLP 0.46875 0.758621
51 PLR 0.467742 0.803571
52 EPC 0.458333 0.810345
53 P0P 0.454545 0.758621
54 PZP 0.439394 0.793103
55 PLP 2KZ 0.435897 0.822581
56 LCS 0.432099 0.671053
57 CAN PLP 0.416667 0.776119
58 0LD 0.412371 0.630952
59 PLP SER 0.402597 0.830508
60 0JO 0.402597 0.707692
61 PPG 0.402299 0.787879
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VD9; Ligand: IN5; Similar sites found: 42
This union binding pocket(no: 1) in the query (biounit: 2vd9.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IXH IMP 0.01013 0.40682 1.38504
2 1ME8 RVP 0.01243 0.41787 1.79028
3 1PVN MZP 0.009896 0.42573 1.8617
4 4QMN DB8 0.01707 0.4091 1.93548
5 4NJH SAM 0.01117 0.41447 2.17391
6 4NJH 2K8 0.01117 0.41447 2.17391
7 2C6Q NDP 0.03204 0.40334 2.2792
8 1JCM 137 0.008042 0.40257 2.3166
9 1TUF AZ1 0.004934 0.4228 2.55754
10 2OO0 PLP 0.007566 0.40171 2.55754
11 3REU ATP 0.005473 0.41004 2.72109
12 5A5W GUO 0.02659 0.4047 2.7668
13 1NJJ ORX 0.01084 0.40221 2.8133
14 1LBF 137 0.007242 0.41807 2.83401
15 5UR1 YY9 0.01213 0.42237 2.89389
16 5TA6 79D 0.005394 0.42404 3.63128
17 1H65 GDP 0.006458 0.41246 3.7037
18 3GLC R5P 0.002913 0.41059 3.72881
19 1W8S FBP 0.003082 0.41462 3.80228
20 5LRT ADP 0.01415 0.40163 3.83632
21 1DQX BMP 0.009104 0.40567 4.11985
22 2I8T GDD 0.01606 0.40052 4.79042
23 2WQP WQP 0.005925 0.42214 5.15759
24 4NAE 1GP 0.006377 0.43235 5.77778
25 4HKP TKW 0.005957 0.41578 6.08974
26 4HKP 16B 0.005446 0.41213 6.08974
27 2Y88 2ER 0.0226 0.40426 6.14754
28 4Q4K FMN 0.01286 0.40501 6.16247
29 4BFM ANP 0.005845 0.41263 6.28743
30 2F6U CIT 0.006055 0.42796 6.41026
31 4R38 RBF 0.006765 0.40976 6.42857
32 3IS2 FAD 0.01831 0.40054 6.49351
33 3KDU NKS 0.03405 0.40523 6.4982
34 2NVA PL2 0.01175 0.40685 6.72043
35 3MI2 PFU 0.03436 0.40579 6.81004
36 2QCD U5P 0.005378 0.41427 7.30769
37 3W9Z FMN 0.004619 0.41535 7.45342
38 3WQD PLP 999 0.00003624 0.49514 7.94872
39 4X6F 3XU 0.02094 0.40885 8.57143
40 2FLI DX5 0.00889 0.40439 9.54545
41 1M5W DXP 0.01967 0.40613 13.1687
42 4V15 PLP 0.001485 0.42423 13.1926
Pocket No.: 2; Query (leader) PDB : 2VD9; Ligand: IN5; 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: 2vd9.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VD9; Ligand: EPC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2vd9.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2VD9; Ligand: EPC; Similar sites found: 27
This union binding pocket(no: 4) in the query (biounit: 2vd9.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ME8 RVP 0.01395 0.41213 1.79028
2 1PVN MZP 0.01172 0.41874 1.8617
3 4QMN DB8 0.01813 0.40462 1.93548
4 4NJH SAM 0.008593 0.41635 2.17391
5 4NJH 2K8 0.008593 0.41635 2.17391
6 1JCM 137 0.006987 0.40168 2.3166
7 1TUF AZ1 0.006197 0.41456 2.55754
8 3REU ATP 0.002339 0.42244 2.72109
9 1LBF 137 0.007765 0.41308 2.83401
10 5UR1 YY9 0.01485 0.41476 2.89389
11 5FLJ QUE 0.003692 0.41961 3.22581
12 1H65 GDP 0.008341 0.40386 3.7037
13 3GLC R5P 0.003241 0.4025 3.72881
14 1W8S FBP 0.001383 0.42356 3.80228
15 1DQX BMP 0.01105 0.40007 4.11985
16 2WQP WQP 0.006632 0.41621 5.15759
17 4NAE 1GP 0.006969 0.43235 5.77778
18 4HKP TKW 0.007716 0.40706 6.08974
19 4HKP 16B 0.00794 0.40119 6.08974
20 2F6U CIT 0.00624 0.42937 6.41026
21 4R38 RBF 0.008132 0.40258 6.42857
22 2NVA PL2 0.01321 0.40112 6.72043
23 2QCD U5P 0.007561 0.40398 7.30769
24 3W9Z FMN 0.005912 0.40683 7.45342
25 3WQD PLP 999 0.00003131 0.50409 7.94872
26 4V15 PLP 0.00166 0.41604 13.1926
27 1QY1 PRZ 0.008529 0.40342 13.2184
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