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;
 submit data
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
Ligand no: 1; Ligand: PDD; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 PDD 1 1
2 PDA 1 1
3 PP3 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 PPD 0.716418 0.918033
9 C6P 0.716418 0.918033
10 ILP 0.710145 0.934426
11 PY5 0.705882 0.890625
12 IN5 0.703125 0.965517
13 7XF 0.685714 0.888889
14 PGU 0.685714 0.888889
15 PDG 0.685714 0.888889
16 KAM 0.68 0.904762
17 QLP 0.676056 0.835821
18 PY6 0.666667 0.892308
19 N5F 0.657534 0.875
20 ORX 0.657534 0.875
21 PLG 0.651515 0.918033
22 PE1 0.648649 0.875
23 76U 0.643836 0.846154
24 CBA 0.638889 0.888889
25 PL4 0.631579 0.875
26 P1T 0.623188 0.875
27 33P 0.614286 0.885246
28 IK2 0.614286 0.846154
29 5PA 0.605634 0.875
30 EA5 0.592105 0.848485
31 PLA 0.589041 0.920635
32 AQ3 0.585366 0.861538
33 PMG 0.565789 0.892308
34 PLP ALO 0.561644 0.916667
35 HEY 0.558442 0.861538
36 PXP 0.555556 0.813559
37 PSZ 0.551282 0.820895
38 3LM 0.551282 0.863636
39 PMP 0.546875 0.881356
40 PMH 0.540541 0.716216
41 GT1 0.538462 0.758065
42 RW2 0.530864 0.820895
43 PXG 0.530864 0.887097
44 PL2 0.525641 0.753623
45 7TS 0.512821 0.723684
46 DCS 0.506329 0.733333
47 9YM 0.506173 0.80303
48 PL8 0.470588 0.753425
49 7B9 0.45977 0.785714
50 PLP 2KZ 0.455696 0.854839
51 KOU 0.448718 0.822581
52 PLR 0.446154 0.775862
53 0JO 0.441558 0.738462
54 PPG 0.436782 0.818182
55 CAN PLP 0.435294 0.80597
56 P0P 0.434783 0.762712
57 1D0 0.428571 0.848485
58 PL6 0.426829 0.75
59 PLP 0.426471 0.762712
60 4LM 0.423077 0.777778
61 PLP SER 0.423077 0.864407
62 Z98 0.421687 0.8
63 EPC 0.421053 0.783333
64 AN7 0.421053 0.766667
65 PZP 0.42029 0.766667
66 LCS 0.416667 0.675325
67 GLY PLP 0.415584 0.803279
68 FOO 0.415584 0.803279
69 0LD 0.414141 0.635294
70 PUS 0.413793 0.684932
71 PLP 2TL 0.407407 0.85
72 PFM 0.404762 0.793651
73 GBC PLP 0.404494 0.84127
74 GAB PLP 0.404494 0.84127
75 5DK 0.4 0.776119
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DAA; Ligand: PDD; Similar sites found: 24
This union binding pocket(no: 1) in the query (biounit: 3daa.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1H82 GZZ 0.0309 0.40513 2.16606
2 1H82 FAD 0.0265 0.40513 2.16606
3 4E3Q PMP 0.01631 0.40502 3.97112
4 3LGS ADE 0.01316 0.42054 6.74157
5 3LGS SAH 0.006444 0.42044 6.74157
6 3GXW SIN 0.01251 0.40465 6.79612
7 5JCM NAD 0.04277 0.40008 6.85921
8 5JCM FAD 0.04163 0.40008 6.85921
9 5JCM ISD 0.04277 0.40008 6.85921
10 3RF4 FUN 0.02252 0.40625 7.75862
11 4JOB TLA 0.01194 0.40014 8.66426
12 1TMX BEZ 0.01706 0.40814 9.02527
13 1RZM E4P 0.02776 0.40111 10.1083
14 4Q3F TLA 0.01588 0.41973 13.6752
15 3UZO GLU 0.000000003564 0.67196 17.3285
16 3UZO PLP 0.000000001189 0.60466 17.3285
17 1OFL NGK GCD 0.02144 0.40822 17.3285
18 5BWX 4W4 0.000000005897 0.49017 20.5776
19 5U3F 7TS 0.0000000003042 0.70427 21.2996
20 5K3W PLP 0.0000000002642 0.65808 35.7401
21 1I2L DCS 0.000000006459 0.65729 39.777
22 4UUG PXG 0.00000000005685 0.74525 49.0975
23 4CE5 PDG 0.00000000007797 0.74268 49.0975
24 1IYE PGU 0.00000000001909 0.78391 49.8195
Pocket No.: 2; Query (leader) PDB : 3DAA; Ligand: PDD; 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: 3daa.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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