Receptor
PDB id Resolution Class Description Source Keywords
6C2Q 2.17 Å EC: 4.2.1.22 CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE FROM SACCH CEREVISIAE: THE STRUCTURE OF THE PLP-L-SERINE INTERMEDIATE 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
PGE A:507;
A:508;
 Invalid;
Invalid;
 none;
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...
EDO A:509;
A:511;
A:510;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
EVM A:501;
 Valid;
 none;
 submit data
333.211 C11 H14 N2 O8 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: EVM; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 EVM 1 1
2 0JO 0.637681 0.85
3 4LM 0.637681 0.833333
4 KOU 0.619718 0.982143
5 FEV 0.619718 0.819672
6 F0G 0.605634 0.877193
7 EPC 0.571429 0.842105
8 PL6 0.565789 0.864407
9 EXT 0.56338 0.847458
10 FEJ 0.558442 0.896552
11 Z98 0.558442 0.825397
12 AN7 0.549296 0.793103
13 PLP 0.546875 0.821429
14 FOO 0.541667 0.830508
15 MPM 0.540541 0.830508
16 PZP 0.538462 0.824561
17 P3D 0.526316 0.78125
18 HCP 0.526316 0.790323
19 6DF 0.525641 0.79661
20 P70 0.52439 0.87931
21 PUS 0.52439 0.779412
22 PL5 0.52439 0.822581
23 EQJ 0.505882 0.828125
24 5DK 0.505882 0.828125
25 GLY PLP 0.5 0.827586
26 P89 0.494118 0.735294
27 SER PLP 0.493671 0.928571
28 PFM 0.481481 0.790323
29 PLP ABU 0.481481 0.816667
30 Q0P 0.477778 0.809524
31 PLP ALO 0.469136 0.877193
32 PLT 0.467391 0.809524
33 PLP 999 0.463415 0.877193
34 PLP PUT 0.45679 0.777778
35 LUH 0.454545 0.757143
36 LUK 0.454545 0.757143
37 O1G 0.449438 0.825397
38 PXP 0.449275 0.810345
39 PMP 0.442857 0.786885
40 PLG 0.441558 0.796875
41 CKT 0.4375 0.9
42 PLP PHE 0.433333 0.844828
43 PLR 0.432836 0.741379
44 PLS 0.432099 0.854839
45 9TD 0.428571 0.768116
46 PDD 0.425 0.809524
47 PDA 0.425 0.809524
48 P1T 0.425 0.787879
49 PP3 0.425 0.809524
50 L7N 0.423529 0.739726
51 GT1 0.416667 0.725806
52 TLP 0.414634 0.83871
53 2BO 0.414634 0.83871
54 2BK 0.414634 0.83871
55 PPG 0.411111 0.815385
56 C6P 0.409639 0.825397
57 PPD 0.409639 0.825397
58 PLP MYB 0.408602 0.73913
59 PMG 0.406977 0.753623
60 PY5 0.404762 0.776119
61 P0P 0.402778 0.821429
62 IK2 0.402439 0.787879
63 HEY 0.402299 0.75
64 PLP PVH 0.4 0.761194
Similar Ligands (3D)
Ligand no: 1; Ligand: EVM; Similar ligands found: 24
No: Ligand Similarity coefficient
1 PLP SER 0.9563
2 PLI 0.9368
3 PLP CYS 0.9365
4 MET PLP 0.9363
5 PLP MET 0.9344
6 5PA 0.9281
7 DCS 0.9269
8 7TS 0.9230
9 PM9 0.9188
10 IN5 0.9155
11 7XF 0.9080
12 LCS 0.9073
13 ILP 0.9069
14 PLP 2TL 0.9015
15 PLP GLY 0.8989
16 PLP 2ML 0.8988
17 PMH 0.8946
18 KET 0.8842
19 PLP 2KZ 0.8842
20 PLA 0.8682
21 3LM 0.8616
22 PGU 0.8568
23 07U 0.8562
24 P19 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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