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Receptor
PDB id Resolution Class Description Source Keywords
1M5W 1.96 Å NON-ENZYME: OTHER 1.96 A CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE COMPLEX WITH 1-DEOXY-D-XYLULOSE PHOSPHATE ESCHERICHIA COLI TIM BARREL PROTEIN-SUBSTRATE COMPLEX MULTI-BINDING STATESBIOSYNTHETIC PROTEIN
Ref.: MULTISTATE BINDING IN PYRIDOXINE 5'-PHOSPHATE SYNTH A CRYSTAL STRUCTURE IN COMPLEX WITH 1-DEOXY-D-XYLUL PHOSPHATE BIOCHEMISTRY V. 41 11649 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DXP A:1001;
B:1002;
C:1003;
E:1005;
F:1006;
G:1007;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 54 uM
214.11 C5 H11 O7 P CC(=O...
PO4 A:1101;
C:1103;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1M5W 1.96 Å NON-ENZYME: OTHER 1.96 A CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE COMPLEX WITH 1-DEOXY-D-XYLULOSE PHOSPHATE ESCHERICHIA COLI TIM BARREL PROTEIN-SUBSTRATE COMPLEX MULTI-BINDING STATESBIOSYNTHETIC PROTEIN
Ref.: MULTISTATE BINDING IN PYRIDOXINE 5'-PHOSPHATE SYNTH A CRYSTAL STRUCTURE IN COMPLEX WITH 1-DEOXY-D-XYLUL PHOSPHATE BIOCHEMISTRY V. 41 11649 2002
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 1M5W Kd = 54 uM DXP C5 H11 O7 P CC(=O)[C@H....
2 1HO4 - PXP C8 H12 N O6 P Cc1c(c(c(c....
3 1IXO - G3P C3 H9 O6 P C([C@H](CO....
4 1IXN - G3P C3 H9 O6 P C([C@H](CO....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 1M5W Kd = 54 uM DXP C5 H11 O7 P CC(=O)[C@H....
2 1HO4 - PXP C8 H12 N O6 P Cc1c(c(c(c....
3 1IXO - G3P C3 H9 O6 P C([C@H](CO....
4 1IXN - G3P C3 H9 O6 P C([C@H](CO....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 1M5W Kd = 54 uM DXP C5 H11 O7 P CC(=O)[C@H....
2 1HO4 - PXP C8 H12 N O6 P Cc1c(c(c(c....
3 1IXO - G3P C3 H9 O6 P C([C@H](CO....
4 1IXN - G3P C3 H9 O6 P C([C@H](CO....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DXP; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 DXP 1 1
2 DEZ 0.628571 0.861111
3 DER 0.628571 0.861111
4 5RP 0.578947 0.815789
5 HMS 0.578947 0.815789
6 5SP 0.578947 0.815789
7 XBP 0.564103 0.861111
8 RUB 0.564103 0.861111
9 RES 0.564103 0.645833
10 HG3 0.515152 0.852941
11 PA5 0.5 0.861111
12 R10 0.5 0.861111
13 E4P 0.486486 0.939394
14 M2P 0.485714 0.833333
15 GOS 0.485714 0.833333
16 6PG 0.47619 0.861111
17 LG6 0.47619 0.861111
18 F6R 0.47619 0.837838
19 TG6 0.47619 0.837838
20 4TP 0.475 0.72093
21 LX1 0.473684 0.885714
22 1GP 0.457143 0.828571
23 G3P 0.457143 0.828571
24 P6T 0.454545 0.861111
25 2FP 0.454545 0.861111
26 I22 0.454545 0.837838
27 P6F 0.454545 0.861111
28 PAN 0.454545 0.645833
29 9C2 0.444444 0.632653
30 TX4 0.439024 0.604167
31 LXP 0.435897 0.763158
32 A5P 0.435897 0.763158
33 DX5 0.435897 0.763158
34 3PG 0.432432 0.911765
35 LRY 0.428571 0.727273
36 D5X 0.428571 0.970588
37 S6P 0.425 0.783784
38 KD0 0.413043 0.861111
39 DG6 0.404762 0.74359
40 R52 0.404762 0.885714
41 R5P 0.404762 0.885714
42 D8X 0.404255 0.820513
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 77
This union binding pocket(no: 1) in the query (biounit: 1m5w.bio4) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1LBT T80 None
2 6APL C5P 1.64609
3 4HWS 1B3 2.05761
4 3MJY IJZ 2.46914
5 4WZH FMN 2.46914
6 4V15 PLP 2.46914
7 1ADO 13P 2.46914
8 4LUT DCS 2.46914
9 3MJY FMN 2.46914
10 3NUB UD0 3.29218
11 3DR4 G4M 3.29218
12 3GD9 GLC BGC BGC BGC 3.29218
13 4JIQ 1L5 3.29218
14 4JIQ FMN 3.29218
15 2C91 NAP 3.5503
16 6B0K 9RN G4S 9RN G4S 3.7037
17 1QXW M1C 3.7037
18 5XFV FMN 3.7037
19 3B0P FMN 3.7037
20 6F30 UD1 3.7037
21 1IR1 CAP 3.7037
22 4UTW RFW 3.93013
23 4UTU LRY 3.93013
24 5A5W GUO 3.95257
25 3WQD PLP 999 4.11523
26 4QYS PLP SEP 4.11523
27 1OX5 1PR 4.11523
28 3A5Z KAA 4.18848
29 5CSS G3P 4.42478
30 4NAE 1GP 4.44444
31 5KY3 GFB 4.52675
32 6AM8 PLT 4.52675
33 2Q8Z NUP 4.93827
34 1WKM MET 4.93827
35 4ZOW CLM 4.93827
36 1WDD CAP 4.93827
37 4HKP TKW 5.34979
38 2QCD U5P 5.34979
39 4HKP 16B 5.34979
40 3CTL S6P 5.62771
41 2V63 CAP 5.76132
42 2VDH CAP 5.76132
43 2V6A CAP 5.76132
44 1GK8 CAP 5.76132
45 1UZH CAP 5.76132
46 3C3N FMN 5.76132
47 2V67 CAP 5.76132
48 1PCA VAL 5.76132
49 1IR2 CAP 5.76132
50 2V68 CAP 5.76132
51 1UZD CAP 5.76132
52 3OVR 5SP 6.14035
53 5FBF DCM 6.17284
54 2FFC U5P 6.58436
55 1N62 MCN 7.22892
56 1Q6O LG6 7.40741
57 1NIU DCS 7.40741
58 4J56 FAD 8.23045
59 3U2U UDP 8.23045
60 3RO7 TDR 8.64198
61 1DQX BMP 9.0535
62 1RBL CAP 9.17431
63 3C56 PH4 9.46502
64 3KDN CAP 9.87654
65 5N9Z CAP 9.87654
66 1MJH ATP 12.3457
67 5VJE GOS 13.1687
68 3EXS 5RP 13.5747
69 6BU0 IHP 16.0305
70 1LBF 137 16.4609
71 1OVD FMN 16.4609
72 1OVD ORO 16.4609
73 5GVH FMN 16.8724
74 1JCM 137 18.5185
75 2Y88 2ER 20.9877
76 2FLI DX5 23.6364
77 1LOR BMP 27.1605
Pocket No.: 2; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 122
This union binding pocket(no: 2) in the query (biounit: 1m5w.bio4) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 4I9A NCN 1.23457
2 5HWV MBN 1.53846
3 1QY1 PRZ 1.72414
4 2OO0 PLP 2.05761
5 3JU6 ANP 2.05761
6 1QDS PGA 2.46914
7 5EZ1 ICB 2.46914
8 5GJO PLP 2.46914
9 2Z6I FMN 2.46914
10 4BI7 PGA 2.46914
11 1LVW TYD 2.46914
12 2F6U CIT 2.5641
13 1LYX PGA 2.88066
14 2Z6J FMN 2.88066
15 3H22 B53 2.88066
16 4EVQ PHB 2.88066
17 4YMZ 13P 2.88066
18 3VNM SDD 2.88066
19 3C8F MT2 3.29218
20 1KKR 2AS 3.29218
21 3UWV 2PG 3.29218
22 1EYE PMM 3.29218
23 2BTM PGA 3.29218
24 3R1Z ALA DGL 3.29218
25 2GMH FAD 3.29218
26 2YPI PGA 3.7037
27 4Z0G 5GP 3.7037
28 1W8S FBP 3.7037
29 2NVA PL2 3.7037
30 1RBO CAP 3.7037
31 4Z87 5GP 3.7037
32 4Q4K FMN 3.92157
33 2VWT PYR 4.11523
34 2C6Q NDP 4.11523
35 3GLC R5P 4.11523
36 4B5W PYR 4.11523
37 2C6Q IMP 4.11523
38 3REU ATP 4.11523
39 3TAO PGH 4.11985
40 3FYP PEP 4.52675
41 1PVN MZP 4.52675
42 1ME8 RVP 4.52675
43 1TRD PGH 4.52675
44 5EYW PGA 4.52675
45 2HJ4 PNZ 4.52675
46 2QUN FUD 4.52675
47 2QF7 AGS 4.52675
48 2RJH DCS 4.52675
49 5AHN IMP 4.70348
50 1SW0 PGA 4.93827
51 2V5K OXM 4.93827
52 3AXK NDP 4.93827
53 1GTE IUR 4.93827
54 1GTE FMN 4.93827
55 4EWN 0VR 5.13834
56 4QPL V3L 5.19481
57 1VKF CIT 5.31915
58 3MI2 PFU 5.34979
59 4NNB OAA 5.34979
60 1QIN GIP 5.46448
61 5T9C G3P 5.76132
62 1MEX RAC 6.10329
63 1EIX BMQ 6.12245
64 5H4S RAM 6.17284
65 6BVE PGA 6.17284
66 3HQP OXL 6.17284
67 1KBI PYR 6.58436
68 1KBI FMN 6.58436
69 2PLK P3D 6.58436
70 1AL8 FMN 6.58436
71 1KBJ FMN 6.58436
72 1AL8 DHP 6.58436
73 1DBT U5P 6.69456
74 4JNJ BTN 6.95652
75 1CX9 NHP 6.99588
76 1FDJ 13P 6.99588
77 6GKV F2W 6.99588
78 1TUF AZ1 6.99588
79 4C1K PEP 6.99588
80 1QPR PPC 6.99588
81 6A63 LAT 7.24638
82 1I7Q BEZ 7.25389
83 2BLE 5GP 7.40741
84 1GVF PGH 7.40741
85 6BKA FMN 7.81893
86 1NJJ ORX 7.81893
87 1TB3 FMN 7.81893
88 3G5N PB2 7.81893
89 4KCT PYR 8.23045
90 4PTN GXV 8.64198
91 1GXU 2HP 8.79121
92 4IXH IMP 9.0535
93 3PPQ CHT 9.0535
94 3JQ3 ADP 9.0535
95 5TCI MLI 9.46502
96 1L5Y BEF 9.67742
97 5J5R IMP 9.76864
98 5J5R 6G1 9.76864
99 3BW2 FMN 9.87654
100 3OIX FMN 9.87654
101 2ZFZ ARG 10.1266
102 4D4U FUC NDG GAL FUC 11.1111
103 4D52 GIV 11.1111
104 1G51 AMO 11.5226
105 1YFS ALA 11.9342
106 4JEJ 1GP 12.3457
107 1ITU CIL 12.3457
108 2OMN IPH 12.4424
109 2VD9 IN5 13.1687
110 2VD9 EPC 13.1687
111 3T7V MD0 13.5802
112 2RDT FMN 13.9918
113 1OFD FMN 13.9918
114 1OFD AKG 13.9918
115 1UJP CIT 14.3911
116 4WOE ADP 16.4609
117 4AF0 IMP 16.8724
118 2G50 PYR 17.6955
119 4IP7 FLC 18.5185
120 3NZ1 3NY 21.8107
121 2OEM 1AE 22.6337
122 1X1Z BMP 27.1605
Pocket No.: 3; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 66
This union binding pocket(no: 3) in the query (biounit: 1m5w.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 3T50 FMN None
2 4AFH L0B None
3 1TV5 FMN 1.23457
4 4H6Q TFB 1.64609
5 1U0A BGC BGC BGC BGC 1.86916
6 3NEM AMO 2.46914
7 2BP1 NDP 2.46914
8 4A22 TD4 2.46914
9 1PZ1 NAP 2.88066
10 2J3M PRI 2.88066
11 2J3M ATP 2.88066
12 1X54 4AD 2.88066
13 2Z6C FMN 3.10078
14 3ATY FMN 3.29218
15 4O12 2QG 3.39321
16 6GBV FMN 3.42466
17 3KRU FMN 3.7037
18 6B5G CQY 4.11523
19 3PC3 P1T 4.11523
20 5XNC N4P 4.11523
21 5L9G MO0 4.52675
22 6B3V ANP 4.52675
23 6B3V 7DQ 4.52675
24 6AMI TRP 4.52675
25 5JIC ADP 4.52675
26 1EP2 ORO 4.93827
27 4ZLU ADP 4.93827
28 4ZLU 4PW 4.93827
29 2HSA FMN 4.93827
30 3T4L ZEA 4.93827
31 1EP2 FMN 4.93827
32 4A3U FMN 4.93827
33 2IRY DGT 5.34979
34 3IES M24 5.34979
35 4WUJ FMN 5.44218
36 4L9Z COA 5.76132
37 4L9Z OXL 5.76132
38 1SES AHX 6.17284
39 3TTC ADP 6.39269
40 1G72 PQQ 6.58436
41 5GVL PLG 6.99588
42 5GVL GI8 6.99588
43 4IGH 1EA 7.40741
44 4IGH FMN 7.40741
45 4IGH ORO 7.40741
46 1UUO BRF 7.40741
47 1UUO ORO 7.40741
48 1UUO FMN 7.40741
49 1VFS DCS 7.40741
50 3W9Z FMN 7.81893
51 5AHM IMP 7.81893
52 1WLE SRP 7.81893
53 1YIQ PQQ 7.81893
54 5ZFJ 9BF 7.92952
55 1V7C HEY 8.23045
56 5FLJ QUE 8.60215
57 3HXU A5A 8.64198
58 1BWV CAP 9.46502
59 3N9R TD3 9.46502
60 3QO8 SSA 10.6996
61 2ZRU FMN 11.1111
62 1UWK NAD 11.1111
63 1UWK URO 11.1111
64 2PR5 FMN 11.3636
65 4R38 RBF 14.2857
66 4J75 TYM 14.4033
Pocket No.: 4; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 85
This union binding pocket(no: 4) in the query (biounit: 1m5w.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5NLD LBT None
2 1QFT HSM None
3 4YLZ LAT NAG GAL None
4 1MFA GLA MMA ABE None
5 5VOP C2F 1.23457
6 1G2O IMH 1.23457
7 4U0I 0LI 1.23457
8 5DEQ ARA 1.75439
9 1P6O HPY 1.86335
10 1C1D PHE 2.05761
11 2V73 SIA 2.09424
12 4AIA ADK 2.12766
13 4JGP PYR 2.30415
14 4B1L FRU 2.42424
15 4RF7 ARG 2.46914
16 4I3G BGC 2.46914
17 1ONX ASP 2.46914
18 1EC9 XYH 2.46914
19 1VBR XYS XYP 2.46914
20 3E3U NVC 2.53807
21 1QAW TRP 2.7027
22 2AL2 PEP 2.88066
23 1ZFJ IMP 2.88066
24 2E7F C2F 2.88066
25 4O1F THG 3.29218
26 3VSS FRU 3.29218
27 4M1U A2G MBG 3.29218
28 1R6W 164 3.29218
29 1VRP ADP 3.7037
30 4BXF AKG 3.7037
31 4XDA RIB 3.7037
32 4M5P MLA 3.7037
33 4NZF ARB 3.7037
34 1SDW IYT 3.7037
35 3NNT DQA 3.7037
36 4Q3S X7A 3.7037
37 3G3N TC8 3.7037
38 2TPS TPS 3.96476
39 4D1J DGJ 4.11523
40 5K0A FAD 4.11523
41 2VEG PMM 4.14013
42 1SJD NPG 4.52675
43 2P8B NSK 4.52675
44 4GN8 ASO 4.52675
45 3A6T 8OG 4.65116
46 4FFG LBS 4.6748
47 4RW3 IPD 4.93827
48 5CC2 CKA 4.93827
49 1AJ8 CIT 4.93827
50 6HKE MLT 5.34591
51 5L2R MLA 5.34979
52 1O5Q PYR 5.76132
53 6I6X H6B 5.76132
54 5FYR INS 5.76132
55 3I7S PYR 6.58436
56 1M3U KPL 6.99588
57 2ZBL BMA 6.99588
58 4LOC OXM 6.99588
59 1SR9 KIV 6.99588
60 2XGT NSS 6.99588
61 1FDJ 2FP 6.99588
62 1REQ DCA 7.81893
63 5TH5 MET 7.81893
64 2JAP J01 7.81893
65 1WAP TRP 8
66 3BJU ATP 8.23045
67 5WS9 OXL 8.64198
68 2YLN CYS 9.0535
69 5MDH MAK 9.46502
70 5A1S FLC 9.87654
71 2BMB PMM 10.2881
72 3E9I XAH 10.2881
73 1O68 KIV 11.9342
74 2YCJ C2F 11.9342
75 2DC1 CIT 12.2881
76 4JX1 CAH 13.9918
77 2RDT 2RD 13.9918
78 1TKK ALA GLU 14.8148
79 5UN9 NHT 16.8724
80 3TYZ PAB 17.6955
81 3TYZ XHP 17.6955
82 1AJ0 SAN 18.107
83 1AJ0 PH2 18.107
84 3DER ALA LYS 18.93
85 5KTQ DCP 18.93
Pocket No.: 5; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 55
This union binding pocket(no: 5) in the query (biounit: 1m5w.bio3) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6EK3 OUL None
2 5EOB 5QQ 1.23457
3 3CXO 3LR 2.05761
4 3CXO 1N5 2.05761
5 1P0Z FLC 2.29008
6 2R0H CTO 2.43902
7 4A59 AMP 2.46914
8 5VLC HSO 2.46914
9 3ZGJ RMN 2.88066
10 5X20 AOT 2.88066
11 3EW2 BTN 2.96296
12 4TVD BGC 3.29218
13 1GQ2 OXL 3.29218
14 3QVL 5HY 3.29218
15 2IMP LAC 3.29218
16 6FEA HCA 3.29218
17 1DRJ RIP 3.7037
18 4CCK OGA 3.7037
19 4NJH SAM 3.91304
20 4NJH 2K8 3.91304
21 1U6R ADP 4.11523
22 3WLV AZA 4.11523
23 1OIJ AKG 4.11523
24 3BMN AX3 4.11523
25 1OIK AKG 4.11523
26 2YFO GLA 4.52675
27 2YFO GAL 4.52675
28 4CW5 FMN 4.52675
29 2WET FAD 4.52675
30 1KJ1 MAN 4.58716
31 1Z44 FMN 4.93827
32 1Z48 FMN 4.93827
33 1Z42 FMN 4.93827
34 2WDQ TEO 4.93827
35 1Z41 FMN 4.93827
36 3P9T TCL 5.02283
37 3DGB MUC 5.34979
38 5OCS FMN 5.34979
39 1IGW PYR 6.58436
40 4CNO 9PY 6.58436
41 1Z6K OAA 6.58436
42 1WUB OTP 6.74157
43 3TUR DGL 6.99588
44 2GQS C2R 7.173
45 1UNQ 4IP 7.2
46 1OF8 PEP 7.40741
47 5Z21 OXM 7.5419
48 3HF3 FMN 7.73639
49 5KJW 53C 7.81893
50 3QMN A3P 9.30233
51 3IWD M2T 10.2941
52 1OFZ FUL 11.9342
53 3VKX T3 13.1687
54 3K4Z CBI 14.4033
55 5M8T 0TR 16.8724
Pocket No.: 6; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 7
This union binding pocket(no: 6) in the query (biounit: 1m5w.bio3) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 5GP0 GPP 1.34228
2 5H9Q TD2 1.93548
3 1GYM MYG 3.7037
4 5TVM PUT 6.99588
5 4KBA 1QM 10.2881
6 2Y69 CHD 11.8421
7 3ANY 2A3 13.5802
Pocket No.: 7; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1m5w.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1m5w.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 2
This union binding pocket(no: 9) in the query (biounit: 1m5w.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1UI0 URA 3.41463
2 3AVR OGA 10.6996
Pocket No.: 10; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 7
This union binding pocket(no: 10) in the query (biounit: 1m5w.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1BXG HCI 2.05761
2 1Q19 SSC 2.88066
3 6C4A PYR 2.88066
4 1U6R IOM 4.11523
5 3DDN HPV 8.23045
6 3G6M CFF 10.2881
7 4W9F 3JU 14.4231
Pocket No.: 11; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 4
This union binding pocket(no: 11) in the query (biounit: 1m5w.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2EG7 OTD 2.88066
2 1ZZ7 S0H 3.0303
3 1DZK PRZ 5.73248
4 2XN2 GLA 5.76132
Pocket No.: 12; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: 4
This union binding pocket(no: 12) in the query (biounit: 1m5w.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1R27 MGD 5.76132
2 2F2T 5IQ 11.1801
3 4B9K TG0 14.4231
4 1WHT BZS 21.5686
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