Receptor
PDB id Resolution Class Description Source Keywords
6C2Z 1.37 Å EC: 4.2.1.22 CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE FROM SACCH CEREVISIAE: THE STRUCTURE OF THE PLP-AMINOACRYLATE INTERMED SACCHAROMYCES CEREVISIAE CBS SYNTHASE PLP LYASE
Ref.: CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE F SACCHAROMYCES CEREVISIAE: ONE ENZYMATIC STEP AT A T BIOCHEMISTRY V. 57 3134 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:513;
A:508;
A:509;
A:511;
A:514;
A:512;
A:510;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
PGE A:507;
 Invalid;
 none;
 submit data
150.173 C6 H14 O4 C(COC...
PEG A:505;
A:506;
 Invalid;
Invalid;
 none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
P1T A:501;
 Valid;
 none;
 submit data
318.22 C11 H15 N2 O7 P Cc1c(...
CL A:504;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
CA A:502;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
NA A:503;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C2Z 1.37 Å EC: 4.2.1.22 CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE FROM SACCH CEREVISIAE: THE STRUCTURE OF THE PLP-AMINOACRYLATE INTERMED SACCHAROMYCES CEREVISIAE CBS SYNTHASE PLP LYASE
Ref.: CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE F SACCHAROMYCES CEREVISIAE: ONE ENZYMATIC STEP AT A T BIOCHEMISTRY V. 57 3134 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6C4P - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 6C2Q - EVM C11 H14 N2 O8 P Cc1c(c(c(c....
3 6C2Z - P1T C11 H15 N2 O7 P Cc1c(c(c(c....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6C4P - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 6C2Q - EVM C11 H14 N2 O8 P Cc1c(c(c(c....
3 6C2Z - P1T C11 H15 N2 O7 P Cc1c(c(c(c....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6C4P - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 6C2Q - EVM C11 H14 N2 O8 P Cc1c(c(c(c....
3 6C2Z - P1T C11 H15 N2 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: P1T; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 P1T 1 1
2 PLG 0.651515 0.890625
3 HEY 0.643836 0.923077
4 3LM 0.635135 0.867647
5 5PA 0.628571 0.878788
6 PDD 0.623188 0.875
7 PP3 0.623188 0.875
8 PDA 0.623188 0.875
9 IK2 0.614286 0.850746
10 2BO 0.605634 0.875
11 2BK 0.605634 0.875
12 TLP 0.605634 0.875
13 PLS 0.605634 0.920635
14 IN5 0.602941 0.84375
15 PPD 0.597222 0.920635
16 C6P 0.597222 0.920635
17 PY5 0.589041 0.865672
18 PLA 0.589041 0.865672
19 LPI 0.586667 0.828571
20 PMG 0.586667 0.84058
21 ILP 0.573333 0.848485
22 7XF 0.573333 0.892308
23 PGU 0.573333 0.892308
24 PDG 0.573333 0.892308
25 CBA 0.573333 0.835821
26 PMP 0.571429 0.825397
27 QLP 0.565789 0.84058
28 PMH 0.561644 0.679487
29 PY6 0.558442 0.84058
30 76U 0.558442 0.850746
31 PXP 0.555556 0.761905
32 N5F 0.551282 0.878788
33 EA5 0.551282 0.852941
34 PSZ 0.551282 0.774648
35 ORX 0.551282 0.878788
36 PL4 0.55 0.878788
37 33P 0.547945 0.80303
38 CKT 0.547945 0.846154
39 PL2 0.545455 0.760563
40 PE1 0.544304 0.878788
41 GT1 0.538462 0.686567
42 KAM 0.536585 0.823529
43 7TS 0.532468 0.753247
44 PXG 0.530864 0.833333
45 0PR 0.530864 0.90625
46 RW2 0.530864 0.909091
47 DN9 0.53012 0.794521
48 PLP 2KZ 0.513158 0.888889
49 DCS 0.506329 0.74026
50 AQ3 0.494253 0.865672
51 PPG 0.488095 0.850746
52 9YM 0.487805 0.808824
53 PL8 0.470588 0.833333
54 RMT 0.465116 0.820895
55 1D0 0.460674 0.826087
56 0JO 0.460526 0.828125
57 7B9 0.45977 0.869565
58 OJQ 0.45 0.6625
59 PLR 0.446154 0.671875
60 AN7 0.44 0.746032
61 FOO 0.434211 0.78125
62 CAN PLP 0.430233 0.8
63 PLP 0.426471 0.714286
64 EVM 0.425 0.787879
65 4LM 0.423077 0.784615
66 PZP 0.42029 0.71875
67 LCS 0.416667 0.683544
68 P0P 0.414286 0.714286
69 FEV 0.4125 0.772727
70 PLP PMP 0.408451 0.78125
71 Z98 0.404762 0.80597
72 GAB PLP 0.404494 0.791045
73 0LD 0.4 0.662791
74 F0G 0.4 0.738462
Similar Ligands (3D)
Ligand no: 1; Ligand: P1T; Similar ligands found: 50
No: Ligand Similarity coefficient
1 PLI 0.9865
2 GLY PLP 0.9845
3 PLP GLY 0.9811
4 PLP SER 0.9742
5 KOU 0.9731
6 SER PLP 0.9672
7 EPC 0.9361
8 PLP 2TL 0.9249
9 PLP CYS 0.9235
10 PLP ALO 0.9233
11 PM9 0.9111
12 AKB PLP 0.9101
13 MET PLP 0.9034
14 PLP MET 0.9024
15 07U 0.8975
16 MPM 0.8934
17 FEJ 0.8911
18 6JJ 0.8905
19 HM5 0.8868
20 7CU 0.8826
21 855 0.8812
22 96X 0.8807
23 66P 0.8804
24 L7N 0.8803
25 KET 0.8792
26 HCP 0.8786
27 8HH 0.8721
28 EAR 0.8720
29 ASP PLP 0.8717
30 SC9 0.8695
31 VKE 0.8688
32 AO6 0.8675
33 6DF 0.8665
34 KB8 0.8664
35 LF5 0.8655
36 LEU PLP 0.8637
37 SCW 0.8632
38 UI2 0.8630
39 5F3 0.8627
40 G16 0.8621
41 BPG 0.8613
42 3QP 0.8595
43 9KQ 0.8587
44 EXT 0.8586
45 2T4 0.8572
46 6SC 0.8565
47 HTJ 0.8559
48 PLP 0A0 0.8554
49 MZC 0.8550
50 IA7 0.8540
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C2Z; Ligand: P1T; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 6c2z.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4JBL MET 49.2625
2 3VC3 C6P 49.4186
3 3VC3 C6P 49.4186
4 3VC3 C6P 49.4186
5 3VC3 C6P 49.4186
6 3VC3 C6P 49.4186
7 3VC3 C6P 49.4186
Pocket No.: 2; Query (leader) PDB : 6C2Z; Ligand: P1T; 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: 6c2z.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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