Receptor
PDB id Resolution Class Description Source Keywords
3L6C 2.2 Å EC: 5.1.1.18 X-RAY CRYSTAL STRUCTURE OF RAT SERINE RACEMASE IN COMPLEX WI MALONATE A POTENT INHIBITOR RATTUS NORVEGICUS PYRIDOXAL PHOSPHATE PLP SERINE RACEMASE ISOMERASE
Ref.: THE STRUCTURE OF MAMMALIAN SERINE RACEMASE: EVIDENC CONFORMATIONAL CHANGES UPON INHIBITOR BINDING. J.BIOL.CHEM. V. 285 12873 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MLI A:341;
B:341;
Valid;
Valid;
none;
none;
submit data
102.046 C3 H2 O4 C(C(=...
MN A:340;
B:340;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
PLP A:350;
B:350;
Part of Protein;
Part of Protein;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3L6C 2.2 Å EC: 5.1.1.18 X-RAY CRYSTAL STRUCTURE OF RAT SERINE RACEMASE IN COMPLEX WI MALONATE A POTENT INHIBITOR RATTUS NORVEGICUS PYRIDOXAL PHOSPHATE PLP SERINE RACEMASE ISOMERASE
Ref.: THE STRUCTURE OF MAMMALIAN SERINE RACEMASE: EVIDENC CONFORMATIONAL CHANGES UPON INHIBITOR BINDING. J.BIOL.CHEM. V. 285 12873 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3L6C - MLI C3 H2 O4 C(C(=O)[O-....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3L6B - MLI C3 H2 O4 C(C(=O)[O-....
2 3L6R - MLI C3 H2 O4 C(C(=O)[O-....
3 3L6C - MLI C3 H2 O4 C(C(=O)[O-....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2GN2 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 2ZR8 - SER C3 H7 N O3 C([C@@H](C....
3 1WTC - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
4 3L6B - MLI C3 H2 O4 C(C(=O)[O-....
5 3L6R - MLI C3 H2 O4 C(C(=O)[O-....
6 3L6C - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MLI; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 MLI 1 1
2 OAA 0.5 0.666667
3 SIN 0.5 0.785714
4 OXL 0.416667 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3L6C; Ligand: MLI; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 3l6c.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F6R FMN 0.02048 0.40143 0.589971
2 3U2U UDP 0.009723 0.44538 1.14068
3 2FCR FMN 0.02095 0.40267 1.15607
4 4B2D FBP 0.004482 0.43979 1.76991
5 4KCT FDP 0.02109 0.40127 1.76991
6 2VCH UDP 0.03223 0.40648 2.0649
7 2FNU PMP UD1 0.04214 0.40516 2.65487
8 2Q4W FAD 0.02686 0.41488 2.94985
9 3HQP FDP 0.02127 0.40272 2.94985
10 2GCO GNP 0.01003 0.4238 2.98507
11 2GCN GDP 0.01421 0.4186 2.98507
12 3WGT FAD 0.02242 0.43361 3.24484
13 3WGT QSC 0.02307 0.43361 3.24484
14 3RDO BTN 0.02977 0.40038 3.26797
15 4N82 FMN 0.01298 0.41316 3.37079
16 4BX7 B4F 0.04309 0.40775 3.7594
17 2NVA PL2 0.01942 0.41688 4.03226
18 3W2E FAD 0.01912 0.43352 4.05904
19 3W2E NAD 0.01912 0.43352 4.05904
20 1AKV FMN 0.0357 0.40084 4.08163
21 3GST GPR 0.02067 0.41603 4.14747
22 5NUL FMN 0.01493 0.40392 4.34783
23 2ALG DAO 0.02653 0.4004 4.34783
24 2ALG HP6 0.02653 0.4004 4.34783
25 4IP7 FBP 0.003219 0.44958 4.42478
26 1U7Z PMT 0.03369 0.41309 4.42478
27 1OW3 GDP 0.01398 0.41419 4.54545
28 1UJ2 C5P 0.02836 0.40428 4.7619
29 5G41 AP5 0.03219 0.42131 4.93274
30 1VG9 GDP 0.01804 0.40213 5.30973
31 1CZR FMN 0.02012 0.40543 5.32544
32 3MN9 ATP 0.01556 0.41059 5.34759
33 1L3I SAH 0.006489 0.4408 5.8997
34 2J0V GDP 0.01572 0.40345 6.13208
35 2Q97 ATP 0.03271 0.40136 6.19469
36 1RYH GNP 0.01078 0.4175 6.40394
37 4DID GDP 0.006956 0.42657 6.78466
38 1A4R GDP 0.01874 0.40953 6.78466
39 1W8S FBP 0.004204 0.43989 6.84411
40 4HDH ATP 0.01523 0.41948 7.37463
41 3P2E SAH 0.0217 0.41299 8
42 1T8U UAP SGN IDS SGN 0.04485 0.41082 8.25959
43 2JFN GLU 0.01755 0.40548 9.12281
44 1AG9 FMN 0.01921 0.40283 9.14286
45 4BMO FMN 0.01881 0.41713 9.2437
46 1GSA ADP 0.03363 0.40702 9.49367
47 1I7Q BEZ 0.01288 0.40546 10.9145
48 3KAP FMN 0.02912 0.40243 12.2449
49 1LFD GNP 0.03035 0.4049 13.7931
50 1I4D GDP 0.01021 0.40873 15.1042
51 1DS6 GDP 0.009914 0.41357 23.9583
52 5IXJ THR 0.000156 0.52906 24.4838
53 3VC3 C6P 0.0001005 0.55023 27.1386
54 3PC3 P1T 0.00002566 0.5694 27.7286
55 1VB3 KPA 0.000005518 0.57483 28.0236
56 4JBL MET 0.00002639 0.48179 29.4985
57 3MN5 ATP 0.03293 0.40135 34.2105
58 1V7C HEY 0.00001927 0.5964 36.8732
59 1D6S PLP MET 0.0001508 0.53305 38.5093
60 1D6S MET PLP 0.0001948 0.52814 38.5093
61 3ZEI AWH 0.008265 0.43175 41.6129
62 2FF3 ATP 0.01892 0.40499 46.6667
Pocket No.: 2; Query (leader) PDB : 3L6C; Ligand: MLI; 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: 3l6c.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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