Receptor
PDB id Resolution Class Description Source Keywords
3DAA 1.9 Å EC: 2.6.1.21 CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE BACILLUS SP. AMINOTRANSFERASE PYRIDOXAL PHOSPHATE TRANSAMINASE
Ref.: CRYSTALLOGRAPHIC STUDY OF STEPS ALONG THE REACTION OF D-AMINO ACID AMINOTRANSFERASE. BIOCHEMISTRY V. 37 4958 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PDD A:285;
B:285;
 Valid;
Valid;
 none;
none;
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320.236 C11 H17 N2 O7 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DAA 1.9 Å EC: 2.6.1.21 CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE BACILLUS SP. AMINOTRANSFERASE PYRIDOXAL PHOSPHATE TRANSAMINASE
Ref.: CRYSTALLOGRAPHIC STUDY OF STEPS ALONG THE REACTION OF D-AMINO ACID AMINOTRANSFERASE. BIOCHEMISTRY V. 37 4958 1998
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3LQS - PSZ C13 H15 N2 O7 P S Cc1c(c(c(c....
2 1DAA - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3DAA - PDD C11 H17 N2 O7 P Cc1c(c(c(c....
4 1A0G - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
5 2DAA - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3LQS - PSZ C13 H15 N2 O7 P S Cc1c(c(c(c....
2 1DAA - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3DAA - PDD C11 H17 N2 O7 P Cc1c(c(c(c....
4 1A0G - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
5 2DAA - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3LQS - PSZ C13 H15 N2 O7 P S Cc1c(c(c(c....
2 1DAA - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3DAA - PDD C11 H17 N2 O7 P Cc1c(c(c(c....
4 1A0G - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
5 2DAA - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PDD; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 PP3 1 1
2 PDA 1 1
3 PDD 1 1
4 TLP 0.753846 0.966102
5 2BO 0.753846 0.966102
6 2BK 0.753846 0.966102
7 PLS 0.727273 0.918033
8 C6P 0.716418 0.918033
9 PPD 0.716418 0.918033
10 ILP 0.710145 0.934426
11 PY5 0.705882 0.890625
12 IN5 0.703125 0.965517
13 PGU 0.685714 0.888889
14 PDG 0.685714 0.888889
15 7XF 0.685714 0.888889
16 KAM 0.68 0.904762
17 LPI 0.676056 0.878788
18 QLP 0.676056 0.835821
19 PY6 0.666667 0.892308
20 N5F 0.657534 0.875
21 ORX 0.657534 0.875
22 0PR 0.653333 0.903226
23 PLG 0.651515 0.918033
24 PE1 0.648649 0.875
25 76U 0.643836 0.846154
26 CBA 0.638889 0.888889
27 PL4 0.631579 0.875
28 P1T 0.623188 0.875
29 33P 0.614286 0.885246
30 IK2 0.614286 0.846154
31 5PA 0.605634 0.875
32 EA5 0.592105 0.848485
33 PLA 0.589041 0.920635
34 AQ3 0.585366 0.861538
35 PMG 0.565789 0.892308
36 HEY 0.558442 0.861538
37 PXP 0.555556 0.813559
38 PSZ 0.551282 0.820895
39 3LM 0.551282 0.863636
40 PMP 0.546875 0.881356
41 PMH 0.540541 0.716216
42 GT1 0.538462 0.758065
43 PXG 0.530864 0.887097
44 RW2 0.530864 0.820895
45 PL2 0.525641 0.753623
46 7TS 0.512821 0.723684
47 DN9 0.511905 0.788732
48 CKT 0.506667 0.870968
49 DCS 0.506329 0.733333
50 9YM 0.506173 0.80303
51 F0G 0.473684 0.816667
52 PL8 0.470588 0.753425
53 7B9 0.45977 0.785714
54 PLP 2KZ 0.455696 0.854839
55 OJQ 0.45 0.697368
56 KOU 0.448718 0.822581
57 PLR 0.446154 0.775862
58 0JO 0.441558 0.738462
59 FEJ 0.439024 0.806452
60 PPG 0.436782 0.818182
61 P0P 0.434783 0.762712
62 RMT 0.431818 0.787879
63 CAN PLP 0.430233 0.794118
64 PLP PMP 0.428571 0.833333
65 1D0 0.428571 0.848485
66 PL6 0.426829 0.75
67 PLP 0.426471 0.762712
68 EVM 0.425 0.809524
69 4LM 0.423077 0.777778
70 Z98 0.421687 0.8
71 EPC 0.421053 0.783333
72 AN7 0.421053 0.766667
73 PZP 0.42029 0.766667
74 PLP SER 0.417722 0.916667
75 LCS 0.416667 0.675325
76 FOO 0.415584 0.803279
77 0LD 0.414141 0.635294
78 PUS 0.413793 0.684932
79 FEV 0.4125 0.765625
80 PFM 0.404762 0.793651
81 GAB PLP 0.404494 0.84127
82 PLP CYS 0.402439 0.857143
83 5DK 0.4 0.776119
84 EQJ 0.4 0.776119
Similar Ligands (3D)
Ligand no: 1; Ligand: PDD; Similar ligands found: 23
No: Ligand Similarity coefficient
1 PLP AOA 0.9569
2 L7N 0.9509
3 PLI 0.9385
4 SER PLP 0.9355
5 MPM 0.9144
6 GLY PLP 0.9102
7 PLP ALO 0.9080
8 PLP GLY 0.9068
9 PLP 2TL 0.9036
10 HM4 0.8842
11 07U 0.8799
12 PLP PUT 0.8776
13 HCP 0.8766
14 ASP PLP 0.8750
15 FBP 0.8731
16 AHG 0.8718
17 4ZK 0.8663
18 PLP 2ML 0.8658
19 IRG 0.8612
20 K6N 0.8598
21 PM9 0.8566
22 855 0.8563
23 ZRM 0.8554
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DAA; Ligand: PDD; Similar sites found with APoc: 11
This union binding pocket(no: 1) in the query (biounit: 3daa.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3UZO PLP 17.3285
2 3UZO PLP 17.3285
3 5U3F 7TS 21.2996
4 5U3F 7TS 21.2996
5 5K3W PLP 35.7401
6 5K3W PLP 35.7401
7 6XU3 PLP 45.8484
8 6XU3 PLP 45.8484
9 6XU3 PLG 45.8484
10 6XU3 PLG 45.8484
11 4UUG PXG 49.0975
Pocket No.: 2; Query (leader) PDB : 3DAA; Ligand: PDD; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 3daa.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3UZO PLP 17.3285
2 3UZO PLP 17.3285
3 5U3F 7TS 21.2996
4 5K3W PLP 35.7401
5 5K3W PLP 35.7401
6 6XU3 PLP 45.8484
7 6XU3 PLP 45.8484
8 6XU3 PLG 45.8484
9 6XU3 PLG 45.8484
10 4UUG PXG 49.0975
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