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 9 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 8 families.
1 2VD9 - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
50% Homology Family (12)
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 1VFT - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
10 2VD9 - EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
11 6SCZ - OJQ C11 H15 N3 O7 P Cc1c(c(c(c....
12 3E5P - PPI C3 H6 O2 CCC(=O)O
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EPC; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 EPC 1 1
2 F0G 0.714286 0.960784
3 KOU 0.676923 0.857143
4 6DF 0.661765 0.941176
5 FEJ 0.652174 0.907407
6 PL6 0.637681 0.872727
7 EXT 0.615385 0.888889
8 PL5 0.608108 0.827586
9 P70 0.608108 0.888889
10 PLP 0.603448 0.862745
11 0JO 0.597015 0.857143
12 4LM 0.597015 0.907407
13 PZP 0.59322 0.901961
14 MPM 0.588235 0.942308
15 PUS 0.586667 0.727273
16 5DK 0.584416 0.774194
17 EQJ 0.584416 0.774194
18 FEV 0.57971 0.890909
19 EVM 0.571429 0.842105
20 HCP 0.571429 0.857143
21 P3D 0.571429 0.783333
22 Z98 0.561644 0.8
23 PLT 0.554217 0.813559
24 PLP ALO 0.547945 0.851852
25 SER PLP 0.534247 0.803571
26 Q0P 0.53012 0.813559
27 AN7 0.529412 0.830189
28 PLP 999 0.52 0.818182
29 FOO 0.5 0.87037
30 P89 0.493827 0.790323
31 LUH 0.487805 0.705882
32 LUK 0.487805 0.705882
33 PLP PHE 0.481928 0.785714
34 O1G 0.481928 0.8
35 GLY PLP 0.479452 0.8
36 PLR 0.47541 0.88
37 PLP PUT 0.473684 0.75
38 PLP ABU 0.461538 0.758621
39 P0P 0.461538 0.826923
40 PFM 0.461538 0.793103
41 IN5 0.458333 0.810345
42 PLP MYB 0.453488 0.686567
43 PXP 0.446154 0.781818
44 PLP PVH 0.443182 0.734375
45 PMP 0.439394 0.789474
46 L7N 0.4375 0.666667
47 GT1 0.432836 0.785714
48 PP3 0.421053 0.783333
49 PDA 0.421053 0.783333
50 PDD 0.421053 0.783333
51 2BK 0.410256 0.783333
52 PLS 0.410256 0.741935
53 TLP 0.410256 0.783333
54 2BO 0.410256 0.783333
55 C6P 0.405063 0.741935
Ligand no: 2; Ligand: IN5; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 IN5 1 1
2 PP3 0.703125 0.965517
3 PDD 0.703125 0.965517
4 PDA 0.703125 0.965517
5 TLP 0.681818 0.932203
6 2BK 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 7XF 0.619718 0.857143
15 PGU 0.619718 0.857143
16 PDG 0.619718 0.857143
17 33P 0.617647 0.915254
18 QLP 0.611111 0.80597
19 LPI 0.611111 0.848485
20 P1T 0.602941 0.84375
21 76U 0.60274 0.815385
22 PY6 0.60274 0.861538
23 ORX 0.594595 0.84375
24 N5F 0.594595 0.84375
25 PE1 0.586667 0.84375
26 5PA 0.585714 0.84375
27 PXP 0.583333 0.842105
28 KAM 0.576923 0.873016
29 PMP 0.57377 0.912281
30 0PR 0.571429 0.870968
31 PL4 0.571429 0.84375
32 IK2 0.571429 0.815385
33 GT1 0.564516 0.783333
34 PMH 0.56338 0.736111
35 CBA 0.554054 0.857143
36 PLA 0.547945 0.888889
37 DCS 0.546667 0.72973
38 7TS 0.533333 0.72
39 EA5 0.532468 0.818182
40 AQ3 0.53012 0.830769
41 PMG 0.526316 0.861538
42 PL2 0.526316 0.776119
43 HEY 0.519481 0.830769
44 3LM 0.512821 0.833333
45 PSZ 0.512821 0.791045
46 9YM 0.506329 0.828125
47 RW2 0.493827 0.791045
48 PXG 0.493827 0.854839
49 PL8 0.487805 0.75
50 7B9 0.47619 0.782609
51 DN9 0.47619 0.760563
52 PLP 0.46875 0.758621
53 PLR 0.467742 0.803571
54 OJQ 0.467532 0.716216
55 CKT 0.466667 0.83871
56 EPC 0.458333 0.810345
57 P0P 0.454545 0.758621
58 PZP 0.439394 0.793103
59 PLP 2KZ 0.435897 0.822581
60 LCS 0.432099 0.671053
61 CAN PLP 0.428571 0.764706
62 PLP PMP 0.426471 0.862069
63 F0G 0.415584 0.783333
64 PLP SER 0.415584 0.883333
65 0LD 0.412371 0.630952
66 0JO 0.402597 0.707692
67 PPG 0.402299 0.787879
68 PLP CYS 0.4 0.825397
Similar Ligands (3D)
Ligand no: 1; Ligand: EPC; Similar ligands found: 22
No: Ligand Similarity coefficient
1 IK2 0.9482
2 PLP AOA 0.9482
3 PLG 0.9406
4 PLI 0.9376
5 DCS 0.9361
6 P1T 0.9361
7 OJQ 0.9338
8 PLP GLY 0.9331
9 5PA 0.9214
10 PMH 0.9205
11 PLP 2TL 0.9177
12 PLP SER 0.9161
13 LCS 0.9154
14 7TS 0.9148
15 PLP CYS 0.8987
16 CKT 0.8823
17 PY5 0.8791
18 ASP PLP 0.8752
19 PPD 0.8752
20 7XF 0.8734
21 ILP 0.8734
22 3LM 0.8572
Ligand no: 2; Ligand: IN5; Similar ligands found: 19
No: Ligand Similarity coefficient
1 PLP AOA 0.9409
2 AN7 0.9346
3 PLI 0.9317
4 SER PLP 0.9298
5 GLY PLP 0.9290
6 PLP ALO 0.9258
7 FOO 0.9235
8 PLP GLY 0.9201
9 L7N 0.9173
10 EVM 0.9155
11 KOU 0.9136
12 4LM 0.9125
13 MPM 0.9118
14 HCP 0.8763
15 PLP 2TL 0.8686
16 07U 0.8685
17 ASP PLP 0.8682
18 KET 0.8682
19 PM9 0.8609
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VD9; Ligand: IN5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2vd9.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2VD9; Ligand: IN5; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VD9; Ligand: EPC; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2VD9; Ligand: EPC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2vd9.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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