Receptor
PDB id Resolution Class Description Source Keywords
4D9C 1.97 Å EC: 4.4.1.15 PMP BOUND FORM OF SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHY OBTAINED AFTER CO-CRYSTALLIZATION WITH L-CYCLOSERINE SALMONELLA TYPHIMURIUM FOLD TYPE II PLP-DEPENDENT ENZYME TRYPTOPHAN SYNTHASE BETA LIKE FAMILY LYASE
Ref.: STRUCTURAL AND MUTATIONAL STUDIES ON SUBSTRATE SPEC AND CATALYSIS OF SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE. PLOS ONE V. 7 36267 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BEN A:401;
C:402;
D:401;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
120.152 C7 H8 N2 [H]/N...
PMP A:402;
B:401;
C:401;
D:402;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
248.173 C8 H13 N2 O5 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D9C 1.97 Å EC: 4.4.1.15 PMP BOUND FORM OF SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHY OBTAINED AFTER CO-CRYSTALLIZATION WITH L-CYCLOSERINE SALMONELLA TYPHIMURIUM FOLD TYPE II PLP-DEPENDENT ENZYME TRYPTOPHAN SYNTHASE BETA LIKE FAMILY LYASE
Ref.: STRUCTURAL AND MUTATIONAL STUDIES ON SUBSTRATE SPEC AND CATALYSIS OF SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE. PLOS ONE V. 7 36267 2012
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4D99 - SER C3 H7 N O3 C([C@@H](C....
2 4D9E - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
3 4D97 - DSN C3 H7 N O3 C([C@H](C(....
4 4D96 - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
5 4D9C - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
6 4D9B - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
70% 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 4D99 - SER C3 H7 N O3 C([C@@H](C....
2 4D9E - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
3 4D97 - DSN C3 H7 N O3 C([C@H](C(....
4 4D96 - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
5 4D9C - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
6 4D9B - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1J0E - 1AC C4 H7 N O2 C1CC1(C(=O....
2 1J0D - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
3 1TZK - 2KT C4 H6 O3 CCC(=O)C(=....
4 1TZJ - A3B C4 H7 N O2 C=C[C@H](C....
5 1TZM - C2N C3 H6 Cl N O2 C([C@H](C(....
6 4D99 - SER C3 H7 N O3 C([C@@H](C....
7 4D9E - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
8 4D97 - DSN C3 H7 N O3 C([C@H](C(....
9 4D96 - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
10 4D9C - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
11 4D9B - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PMP; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 PMP 1 1
2 PXP 0.7 0.888889
3 GT1 0.673077 0.793103
4 PLG 0.57377 0.866667
5 IN5 0.57377 0.912281
6 P1T 0.571429 0.825397
7 PLR 0.557692 0.781818
8 2BO 0.553846 0.881356
9 TLP 0.553846 0.881356
10 2BK 0.553846 0.881356
11 PP3 0.546875 0.881356
12 PDA 0.546875 0.881356
13 PDD 0.546875 0.881356
14 ILP 0.544118 0.852459
15 33P 0.538462 0.896552
16 IK2 0.538462 0.825397
17 5PA 0.530303 0.825397
18 PLS 0.530303 0.866667
19 PMH 0.530303 0.742857
20 PLP 0.527273 0.767857
21 C6P 0.522388 0.866667
22 PPD 0.522388 0.866667
23 ORX 0.521127 0.854839
24 PXM 0.52 0.735849
25 PZP 0.517857 0.836364
26 PLA 0.514706 0.8125
27 PY5 0.514706 0.8125
28 PL2 0.514286 0.84127
29 QLP 0.514286 0.815385
30 PE1 0.513889 0.854839
31 PPG 0.513514 0.825397
32 P0P 0.508772 0.8
33 HEY 0.507042 0.8125
34 CBA 0.5 0.83871
35 PGU 0.5 0.83871
36 7TS 0.5 0.702703
37 EA5 0.5 0.828125
38 3LM 0.5 0.787879
39 PDG 0.5 0.83871
40 7XF 0.5 0.83871
41 9YM 0.493151 0.868852
42 LCS 0.492958 0.675676
43 PMG 0.492958 0.787879
44 DCS 0.492958 0.712329
45 76U 0.486111 0.825397
46 PY6 0.486111 0.787879
47 PL4 0.48 0.854839
48 PSZ 0.479452 0.8
49 N5F 0.479452 0.825397
50 4LM 0.462687 0.725806
51 0JO 0.462687 0.714286
52 AN7 0.461538 0.741379
53 PXG 0.460526 0.866667
54 RW2 0.460526 0.8
55 FOO 0.454545 0.75
56 PL8 0.454545 0.732394
57 GLY PLP 0.454545 0.779661
58 NPL 0.45 0.898305
59 KAM 0.448718 0.825397
60 1D0 0.444444 0.8
61 7B9 0.443038 0.764706
62 2B1 0.443038 0.690141
63 P3D 0.442857 0.85
64 PLP SER 0.441176 0.779661
65 EPC 0.439394 0.789474
66 MP5 0.438596 0.728814
67 EXT 0.432836 0.79661
68 PLP PMP 0.432836 0.770492
69 AQ3 0.426829 0.8125
70 2B6 0.426829 0.662162
71 PLP ALO 0.422535 0.833333
72 MPM 0.414286 0.75
73 KOU 0.408451 0.8
74 SER PLP 0.402778 0.813559
75 HCP 0.402778 0.741935
76 PLP 2TL 0.402778 0.79661
77 Z98 0.4 0.777778
78 PFM 0.4 0.770492
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D9C; Ligand: PMP; Similar sites found: 28
This union binding pocket(no: 1) in the query (biounit: 4d9c.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ZNO SUC 0.005432 0.43209 1.49254
2 3ZV6 NAD 0.007689 0.4111 2.13523
3 3ZV6 4HB 0.008085 0.4111 2.13523
4 3MJY FMN 0.007214 0.40264 2.33918
5 3MJY IJZ 0.007214 0.40264 2.33918
6 3VC3 C6P 0.0004336 0.44379 3.21637
7 3MBI HSX 0.004687 0.44133 3.48432
8 5JSQ 6MS 0.0197 0.40183 4.62963
9 1ZN7 HSX 0.02328 0.40197 5
10 5CX8 TG6 0.0209 0.41964 5.26316
11 5E5U MLI 0.002906 0.40757 5.30303
12 4QYS PLR 0.00006009 0.52338 5.55556
13 4QYS PLP SEP 0.00001065 0.50643 5.55556
14 5F7U GLC GLC 0.01839 0.42036 5.55556
15 5IXJ THR 0.000405 0.45151 6.43275
16 1PZM 5GP 0.02831 0.40151 8.53081
17 3PC3 P1T 0.00006198 0.46278 9.06433
18 5BWD FUM 0.03365 0.40256 10
19 4D9M 0JO 0.00008046 0.47995 11.6959
20 3VPB GLU 0.0141 0.42303 15.9574
21 1V7C HEY 0.000000302 0.57547 16.3743
22 5B3A 0JO 0.0002208 0.46173 17.2515
23 1WAP TRP 0.01745 0.40081 17.3333
24 1D6S MET PLP 0.0002951 0.44453 18.0124
25 1D6S PLP MET 0.0002526 0.44259 18.0124
26 5I7A 68Q 0.007808 0.40337 18.0982
27 3ZEI AWH 0.0001395 0.46887 18.3871
28 5C2N NAG 0.03414 0.40279 18.75
Pocket No.: 2; Query (leader) PDB : 4D9C; Ligand: PMP; 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: 4d9c.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4D9C; Ligand: PMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4d9c.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4D9C; Ligand: PMP; Similar sites found: 18
This union binding pocket(no: 4) in the query (biounit: 4d9c.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5KOD IAC 0.01216 0.42519 1.46199
2 4RDL FUC GAL NDG FUC 0.03591 0.40289 2.5974
3 2YGM GLA NAG GAL FUC 0.03091 0.40092 2.92398
4 5GJC ATP 0.01628 0.41116 3.50877
5 5HWK BEZ 0.01189 0.42786 3.75
6 5H6S HDH 0.03127 0.40277 3.80117
7 1JI0 ATP 0.03774 0.40032 4.16667
8 5HX1 UMP 0.01777 0.41874 4.34783
9 1TV5 ORO 0.03249 0.40422 4.38596
10 4WCX ALA 0.03913 0.4021 4.97076
11 4XZ3 ACP 0.03517 0.40195 5.26316
12 4NAE 1GP 0.03734 0.40041 5.33333
13 5LPG 71V 0.0141 0.41846 5.4878
14 4R2I ANP 0.02962 0.40591 5.71429
15 5LY2 OGA 0.03332 0.40188 7.89474
16 1G8S MET 0.03135 0.40489 8.18713
17 2CBZ ATP 0.02339 0.4082 11.3924
18 4PPF FLC 0.01389 0.42549 12.2807
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