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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: 83
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 2BK 0.553846 0.881356
9 2BO 0.553846 0.881356
10 TLP 0.553846 0.881356
11 PDD 0.546875 0.881356
12 PP3 0.546875 0.881356
13 PDA 0.546875 0.881356
14 ILP 0.544118 0.852459
15 IK2 0.538462 0.825397
16 33P 0.538462 0.896552
17 PMH 0.530303 0.742857
18 5PA 0.530303 0.825397
19 PLS 0.530303 0.866667
20 PLP 0.527273 0.767857
21 PPD 0.522388 0.866667
22 C6P 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 PDG 0.5 0.83871
35 CBA 0.5 0.83871
36 EA5 0.5 0.828125
37 3LM 0.5 0.787879
38 7XF 0.5 0.83871
39 7TS 0.5 0.702703
40 PGU 0.5 0.83871
41 9YM 0.493151 0.868852
42 DCS 0.492958 0.712329
43 PMG 0.492958 0.787879
44 LPI 0.492958 0.776119
45 LCS 0.492958 0.675676
46 76U 0.486111 0.825397
47 PY6 0.486111 0.787879
48 PL4 0.48 0.854839
49 PSZ 0.479452 0.8
50 N5F 0.479452 0.825397
51 0JO 0.462687 0.714286
52 4LM 0.462687 0.725806
53 AN7 0.461538 0.741379
54 PXG 0.460526 0.866667
55 RW2 0.460526 0.8
56 FOO 0.454545 0.75
57 PL8 0.454545 0.732394
58 NPL 0.45 0.898305
59 FEV 0.449275 0.714286
60 KAM 0.448718 0.825397
61 RMT 0.448718 0.765625
62 1D0 0.444444 0.8
63 2B1 0.443038 0.690141
64 7B9 0.443038 0.764706
65 P3D 0.442857 0.85
66 EVM 0.442857 0.786885
67 EPC 0.439394 0.789474
68 MP5 0.438596 0.728814
69 PLP CYS 0.43662 0.836066
70 EXT 0.432836 0.79661
71 AQ3 0.426829 0.8125
72 2B6 0.426829 0.662162
73 MPM 0.414286 0.75
74 F0G 0.414286 0.762712
75 PLP 2TL 0.410959 0.85
76 KOU 0.408451 0.8
77 PLP SEP 0.405405 0.85
78 PLP BH2 0.405405 0.85
79 SEP PLP 0.405405 0.85
80 HCP 0.402778 0.741935
81 LEU PLP 0.4 0.822581
82 Z98 0.4 0.777778
83 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 with APoc: 111
This union binding pocket(no: 1) in the query (biounit: 4d9c.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZNO SUC 1.49254
2 1H5R THM 1.70648
3 3QH2 3NM 1.80995
4 5ORG 6DB 1.90114
5 2AWN ADP 2.04678
6 1H5S TMP 2.04678
7 1MZV AMP 2.12766
8 3ZV6 NAD 2.13523
9 3ZV6 4HB 2.13523
10 6AR9 3L4 2.20588
11 3MJY FMN 2.33918
12 3MJY IJZ 2.33918
13 3U6W KIV 2.33918
14 1SR9 KIV 2.33918
15 4C25 13P 2.35849
16 3JQ7 DX2 2.43056
17 5WBF LAC 2.59259
18 5VJN IR8 2.6738
19 1J1R ADE 2.68199
20 4RKX 3S9 2.68199
21 1UKG MMA 2.77778
22 6B2W AG2 3.003
23 2JK0 ASP 3.07692
24 1O5O U5P 3.16742
25 3QPB URA 3.19149
26 3VC3 C6P 3.21637
27 3HQP FDP 3.21637
28 1ELU PDA 3.33333
29 1C3M MAN MAN 3.40136
30 1DQN IMU 3.47826
31 3MBI HSX 3.48432
32 1QMG DMV 3.50877
33 3P4X ADP 3.50877
34 3SCH TB6 3.53535
35 5H6S HDH 3.80117
36 4B2D FBP 3.80117
37 1VHN FMN 4.08805
38 1KZL CRM 4.32692
39 1YOE RIB 4.34783
40 1GXS DKA 4.43038
41 1TL2 NDG 4.66102
42 3CEV ARG 4.68227
43 3AI8 HNQ 4.6875
44 2JKY 5GP 4.69484
45 2WPB ZZI 4.93421
46 4P83 U5P 4.94506
47 2FN1 SAL 4.97076
48 4IP7 FBP 4.97076
49 4X8N GLU ARG GLU SEP GLU PHE ASP ILE GLU ASP 4.97238
50 3LN9 FLC 5.03597
51 3MKN DNB 5.06329
52 1LVW TYD 5.08475
53 3X44 PUS 5.12048
54 5CX8 TG6 5.26316
55 1E5F PLP 5.26316
56 3LRE ADP 5.26316
57 5E5U MLI 5.30303
58 1VBO MAN MAN MAN 5.36913
59 4QYS PLR 5.55556
60 4QYS PLP SEP 5.55556
61 4CIB 7UZ 5.55556
62 5F7U GLC GLC 5.55556
63 5YRM BGC GLC 5.6338
64 5YRL GLC GLC 5.6338
65 1WHT BZS 5.85938
66 5K8P 6R8 6.14035
67 2CXG GLC GLC 6.14035
68 6AM8 PLT 6.43275
69 6CUZ FEV 6.43275
70 6AM8 TRP 6.43275
71 6AMI TRP 6.43275
72 4JLS 3ZE 6.57895
73 3EJ0 11X 6.63265
74 2JBH 5GP 6.66667
75 4JBL MET 6.78466
76 1YKJ PHB 7.01754
77 1P19 IMP 7.23982
78 3N2O AG2 7.30994
79 2JFQ DGL 7.34266
80 2RI1 GLP 7.65957
81 5YRJ BGC GLC 7.74648
82 2YKX AKG 8.18713
83 3KIH GDL 8.24742
84 6C2Z P1T 8.47953
85 3KIF GDL 8.49057
86 1PZM 5GP 8.53081
87 3CL7 HYN 8.76623
88 3PC3 P1T 9.06433
89 4HNN LYS 9.24856
90 5BWD FUM 10
91 2C3H GLC GLC 10.2041
92 1CX9 NHP 11.1111
93 4D9M 0JO 11.6959
94 1FWV SGA MAG FUC 11.9403
95 1UPF URF 12.5
96 2DWU DGL 13.4058
97 5ZCO CHD 14.2857
98 1XTT U5P 14.3519
99 3VPB GLU 15.9574
100 4V1F BQ1 16.2791
101 1V7C HEY 16.3743
102 5B3A 0JO 17.2515
103 1WAP TRP 17.3333
104 1D6S MET PLP 18.0124
105 1D6S PLP MET 18.0124
106 5I7A 68Q 18.0982
107 3ZEI AWH 18.3871
108 5D85 P1T 18.4049
109 5C2N NAG 18.75
110 3L6R MLI 19.3642
111 2VGD XYP XYP 20.1835
Pocket No.: 2; Query (leader) PDB : 4D9C; Ligand: PMP; Similar sites found with APoc: 33
This union binding pocket(no: 2) in the query (biounit: 4d9c.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2GNK ATP None
2 2UVO NAG 1.16959
3 5V8E CIT 1.61812
4 1O9W NAG 1.69492
5 3B8I OXL 1.74216
6 5LA1 XYP 2.33918
7 5T96 79J 2.33918
8 5NDB 8TW 2.4
9 6HKE LMR 2.51572
10 4WZH FMN 2.63158
11 1ME8 RVP 2.92398
12 2Z4T C5P 3.21637
13 1GPM AMP 3.80117
14 1HGX 5GP 3.82514
15 4JEJ 1GP 4.09836
16 5ZKC 3C0 4.97076
17 3ACC 5GP 4.97238
18 3O5N BR0 5.35714
19 4P5E N6P 5.92105
20 1QAW TRP 8.10811
21 3BY8 MLT 8.4507
22 3ZZS TRP 9.23077
23 1NSA BEN 9.64912
24 2ZFZ ARG 10.1266
25 1KGZ PRP 10.2339
26 4P86 5GP 10.929
27 3L6C MLI 11.5044
28 5TCI MLI 11.9883
29 3AXM 6PG 12.4031
30 1IYB 5GP 13.4615
31 4USI AKG 14.9351
32 2Z48 NGA 15.2047
33 5D63 FUC GLA GLA 20.4778
Pocket No.: 3; Query (leader) PDB : 4D9C; Ligand: PMP; Similar sites found with APoc: 11
This union binding pocket(no: 3) in the query (biounit: 4d9c.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5H4S RAM 1.76056
2 3JQG AX6 2.43056
3 4RDL FUC GAL NDG FUC 2.5974
4 1Q8S MAN MMA 2.77778
5 4D52 GXL 3.1746
6 4MIB 28M 3.21637
7 1IXE CIT 3.50877
8 1GPM CIT 3.80117
9 2VHL GLP 4.09357
10 4XFR CIT 4.21546
11 2NU5 NAG 7.37705
Pocket No.: 4; Query (leader) PDB : 4D9C; Ligand: PMP; Similar sites found with APoc: 105
This union binding pocket(no: 4) in the query (biounit: 4d9c.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5KOD IAC 1.46199
2 2VVG ADP 1.46199
3 5KL0 G16 1.75439
4 3W9F I3P 1.92308
5 3WIR BGC 2.04678
6 3T3Z 9PL 2.04678
7 2PZE ATP 2.18341
8 3AB4 LYS 2.24719
9 5WKC TP9 2.33918
10 4FRZ ADP 2.33918
11 2NNJ 225 2.33918
12 5A1S FLC 2.33918
13 2I4O ATP 2.33918
14 3BMN AX3 2.43056
15 2W58 ADP 2.47525
16 6HKE MLT 2.51572
17 3NHB ADP 2.61438
18 1V8K ANP 2.63158
19 5YV5 ADP 2.63158
20 1YQT ADP 2.63158
21 2I6U NVA 2.63158
22 1RRC ADP 2.65781
23 1Q8Q MAN MMA 2.77778
24 2PHX MAN MAN 2.77778
25 1Q8V MAN MAN 2.77778
26 2PHX MAN MAN MAN MAN 2.77778
27 4U00 ADP 2.86885
28 3U40 ADN 2.89256
29 2XT3 ADP 2.92398
30 2YGM GLA NAG GAL FUC 2.92398
31 5NC1 NAG 2.95359
32 4HE2 AMP 2.95858
33 2W14 WR2 2.9703
34 3COB ADP 3.21637
35 2R68 SUP 3.21637
36 6F5W KG1 3.21637
37 2BO4 FLC 3.21637
38 5E9G GLV 3.21637
39 1Y63 ADP 3.26087
40 1G6H ADP 3.50195
41 2DVZ GLU 3.50877
42 1Y9G FRU 3.50877
43 1PVN MZP 3.7234
44 5HWK BEZ 3.75
45 2J0W ASP 3.78619
46 3A4M ADP 3.84615
47 1OIK AKG 3.98671
48 1JI0 ATP 4.16667
49 5HX1 UMP 4.34783
50 6EBQ FMN 4.375
51 3QTP 2PG 4.38596
52 1TV5 ORO 4.38596
53 3W5J GDP 4.41176
54 1GXS BEZ 4.43038
55 4WOP CTP 4.44444
56 4N82 FMN 4.49438
57 4BJH PAL 4.65839
58 1XX6 ADP 4.71204
59 2V2G BEZ 4.72103
60 1BG2 ADP 4.92308
61 2FN1 PYR 4.97076
62 4WCX ALA 4.97076
63 1T5C ADP 5.15759
64 3H4S ADP 5.18518
65 4XZ3 ACP 5.26316
66 4NAE 1GP 5.33333
67 5LPG 71V 5.4878
68 2DC1 CIT 5.50847
69 3VY6 BGC BGC 5.67376
70 4DDY DN6 5.70342
71 4R2I ANP 5.71429
72 6C0B MLI 5.84795
73 4E3Q PMP 6.43275
74 3R7F CP 6.43275
75 3CYQ AMU 6.52174
76 3RC3 ANP 7.01754
77 2D2F ADP 7.2
78 5BSH PRO 7.22022
79 4ARE FLC 7.30994
80 2HYQ MAN MAN 7.37705
81 5YRG BGC GLC 7.74648
82 3HRD NIO 7.77027
83 5LY2 OGA 7.89474
84 3ZW2 NAG GAL FUC 8.04598
85 1NC2 DOE 8.1448
86 3OQJ 3CX 8.17121
87 1G8S MET 8.18713
88 2Y65 ADP 8.47953
89 2F5X ASP 8.97436
90 1XXA ARG 8.97436
91 2NZU BG6 9.09091
92 6F1J EDG 9.53846
93 2KIN ADP 10
94 1LVG ADP 10.101
95 2CBZ ATP 11.3924
96 3F6R FMN 11.4865
97 4PPF FLC 12.2807
98 3W6G FLC 12.963
99 5Z84 CHD 14.2857
100 6BTP E8J 15.4229
101 5TSH ADP 16.3743
102 1JJ7 ADP 19.2308
103 5ZMY TAR 20.7006
104 2CUN 3PG 22.2222
105 4QM7 GTP 29.2398
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