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Receptor
PDB id Resolution Class Description Source Keywords
5CKS 2.12 Å EC: 4.1.2.15 DAHP (3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE) SYNTHASE I WITH DAHP OXIME. ESCHERICHIA COLI (STRAIN K12) DAHP SYNTHASE INHIBITOR COMPLEX TRANSITION STATE MIMIC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: POTENT INHIBITION OF 3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE (DAHP) S BY DAHP OXIME, A PHOSPHATE GROUP MIMIC. BIOCHEMISTRY V. 55 6617 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GAL B:401;
A:401;
C:401;
Invalid;
Valid;
Invalid;
none;
none;
none;
submit data
180.156 C6 H12 O6 C([C@...
52L C:402;
B:402;
Valid;
Valid;
none;
none;
Ki = 1.5 uM
303.161 C7 H14 N O10 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CKS 2.12 Å EC: 4.1.2.15 DAHP (3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE) SYNTHASE I WITH DAHP OXIME. ESCHERICHIA COLI (STRAIN K12) DAHP SYNTHASE INHIBITOR COMPLEX TRANSITION STATE MIMIC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: POTENT INHIBITION OF 3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE (DAHP) S BY DAHP OXIME, A PHOSPHATE GROUP MIMIC. BIOCHEMISTRY V. 55 6617 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
2 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
3 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
10 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
11 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1OAB - PEP C3 H5 O6 P C=C(C(=O)O....
10 1OFO - PGA C2 H5 O6 P C(C(=O)O)O....
11 1OF6 - DTY C9 H11 N O3 c1cc(ccc1C....
12 1OF8 - G3P C3 H9 O6 P C([C@H](CO....
13 1OFA - PEP C3 H5 O6 P C=C(C(=O)O....
14 1HFB - PEP C3 H5 O6 P C=C(C(=O)O....
15 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
16 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
17 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GAL; Similar ligands found: 142
No: Ligand ECFP6 Tc MDL keys Tc
1 WOO 1 1
2 GLC 1 1
3 BGC 1 1
4 ALL 1 1
5 BMA 1 1
6 GXL 1 1
7 GIV 1 1
8 GAL 1 1
9 MAN 1 1
10 GLA 1 1
11 Z6J 0.653846 0.866667
12 32O 0.653846 0.866667
13 RIB 0.653846 0.866667
14 FUB 0.653846 0.866667
15 AHR 0.653846 0.866667
16 MLB 0.511628 0.848485
17 GLC GLC 0.511628 0.848485
18 BGC GLC 0.511628 0.848485
19 BGC GLA 0.511628 0.848485
20 GLA BMA 0.511628 0.848485
21 MAN BMA 0.511628 0.848485
22 BMA GLA 0.511628 0.848485
23 GLA BGC 0.511628 0.848485
24 MAN MAN 0.511628 0.848485
25 GLA GLC 0.511628 0.848485
26 BMA MAN 0.511628 0.848485
27 GAL GLC 0.511628 0.848485
28 GAL GAL 0.511628 0.848485
29 LAK 0.511628 0.848485
30 GLC BGC 0.511628 0.848485
31 YDR 0.5 0.8
32 GLC GLC GLC GLC BGC 0.488889 0.848485
33 GLC GLC GLC 0.488889 0.848485
34 MAN MAN MAN 0.488889 0.848485
35 BMA MAN MAN 0.488889 0.848485
36 GLC GLC GLC GLC GLC BGC 0.488889 0.848485
37 EMZ 0.472222 0.794118
38 BG6 0.461538 0.675
39 BGP 0.461538 0.675
40 G6P 0.461538 0.675
41 M6P 0.461538 0.675
42 M6D 0.461538 0.675
43 A6P 0.461538 0.675
44 GAF 0.457143 0.875
45 SHG 0.457143 0.875
46 2FG 0.457143 0.875
47 G2F 0.457143 0.875
48 2H5 0.457143 0.875
49 GCS 0.457143 0.777778
50 1GN 0.457143 0.777778
51 X6X 0.457143 0.777778
52 PA1 0.457143 0.777778
53 95Z 0.457143 0.777778
54 G3F 0.457143 0.875
55 NGR 0.454545 0.848485
56 MAL 0.454545 0.848485
57 MAN GLC 0.454545 0.848485
58 GAL BGC 0.454545 0.848485
59 GLA GLA 0.454545 0.848485
60 BGC BMA 0.454545 0.848485
61 M3M 0.454545 0.848485
62 GLA GAL 0.454545 0.848485
63 MAB 0.454545 0.848485
64 GLC GAL 0.454545 0.848485
65 B2G 0.454545 0.848485
66 LBT 0.454545 0.848485
67 BMA GAL 0.454545 0.848485
68 LAT 0.454545 0.848485
69 BGC GAL 0.454545 0.848485
70 CBI 0.454545 0.848485
71 CBK 0.454545 0.848485
72 N9S 0.454545 0.848485
73 LB2 0.454545 0.848485
74 3MG 0.444444 0.875
75 TCB 0.444444 0.8
76 GLC SGC 0.444444 0.8
77 YIO 0.441176 0.870968
78 2GS 0.432432 0.875
79 2M4 0.431818 0.848485
80 AHR AHR 0.428571 0.764706
81 GLF 0.428571 0.84375
82 FUB AHR 0.428571 0.764706
83 MAN BMA BMA 0.416667 0.848485
84 BMA MAN BMA 0.416667 0.848485
85 CTR 0.416667 0.848485
86 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.848485
87 GLA GAL BGC 0.416667 0.848485
88 CE5 0.416667 0.848485
89 MLR 0.416667 0.848485
90 CE6 0.416667 0.848485
91 MT7 0.416667 0.848485
92 BMA BMA BMA 0.416667 0.848485
93 GLC BGC BGC BGC BGC 0.416667 0.848485
94 MAN MAN BMA BMA BMA BMA 0.416667 0.848485
95 BGC BGC BGC BGC BGC 0.416667 0.848485
96 BGC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
97 BGC GLC GLC 0.416667 0.848485
98 BMA BMA BMA BMA BMA 0.416667 0.848485
99 MAN BMA BMA BMA BMA 0.416667 0.848485
100 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
101 GLC BGC BGC BGC BGC BGC 0.416667 0.848485
102 MAN BMA BMA BMA BMA BMA 0.416667 0.848485
103 BGC BGC BGC BGC BGC BGC 0.416667 0.848485
104 BGC GLC GLC GLC 0.416667 0.848485
105 BGC BGC BGC GLC 0.416667 0.848485
106 CTT 0.416667 0.848485
107 GLA GAL GLC 0.416667 0.848485
108 MTT 0.416667 0.848485
109 GLC BGC BGC BGC 0.416667 0.848485
110 GLC GLC BGC 0.416667 0.848485
111 CEY 0.416667 0.848485
112 B4G 0.416667 0.848485
113 CE8 0.416667 0.848485
114 BMA BMA BMA BMA BMA BMA 0.416667 0.848485
115 GAL FUC 0.416667 0.848485
116 DXI 0.416667 0.848485
117 GLC BGC GLC 0.416667 0.848485
118 CT3 0.416667 0.848485
119 GAL GAL GAL 0.416667 0.848485
120 GLC GLC GLC GLC GLC 0.416667 0.848485
121 BGC BGC BGC BGC 0.416667 0.848485
122 BGC BGC BGC 0.416667 0.848485
123 BGC BGC GLC 0.416667 0.848485
124 CEX 0.416667 0.848485
125 GLC GAL GAL 0.416667 0.848485
126 BGC GLC GLC GLC GLC 0.416667 0.848485
127 GLC BGC BGC 0.416667 0.848485
128 GS1 GLC GS1 0.408163 0.8
129 SGC SGC BGC 0.408163 0.8
130 BGC BGC BGC GLC BGC BGC 0.408163 0.848485
131 GLC BGC BGC BGC BGC BGC BGC 0.408163 0.848485
132 1LL 0.405405 0.771429
133 TDG 0.405405 0.771429
134 TRE 0.405405 0.848485
135 NDG 0.404762 0.7
136 NGA 0.404762 0.7
137 NAG 0.404762 0.7
138 HSQ 0.404762 0.7
139 A2G 0.404762 0.7
140 BM3 0.404762 0.7
141 FUB AHR AHR 0.4 0.764706
142 AHR AHR AHR AHR AHR AHR 0.4 0.764706
Ligand no: 2; Ligand: 52L; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 52L 1 1
2 LXP 0.511628 0.680851
3 A5P 0.511628 0.680851
4 DX5 0.511628 0.680851
5 KD0 0.510204 0.755556
6 R10 0.5 0.755556
7 PA5 0.5 0.755556
8 M2P 0.487805 0.695652
9 GOS 0.487805 0.695652
10 6PG 0.479167 0.755556
11 LG6 0.479167 0.755556
12 DG6 0.478261 0.666667
13 I22 0.46 0.702128
14 TG6 0.44898 0.702128
15 F6R 0.44898 0.702128
16 TX4 0.446809 0.745098
17 LX1 0.444444 0.659574
18 FQ8 0.44 0.702128
19 DEZ 0.434783 0.755556
20 DER 0.434783 0.755556
21 S6P 0.434783 0.659574
22 P6T 0.431373 0.717391
23 2FP 0.431373 0.717391
24 PAN 0.431373 0.784314
25 P6F 0.431373 0.717391
26 9C2 0.423077 0.703704
27 R5P 0.416667 0.733333
28 R52 0.416667 0.733333
29 4TP 0.416667 0.791667
30 5RP 0.408163 0.723404
31 HMS 0.408163 0.723404
32 5SP 0.408163 0.723404
33 HG3 0.404762 0.666667
34 G6Q 0.4 0.733333
35 AGP 0.4 0.72
36 M6R 0.4 0.72
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CKS; Ligand: 52L; Similar sites found with APoc: 37
This union binding pocket(no: 1) in the query (biounit: 5cks.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2J62 GSZ 1.7094
2 3GDN MXN 1.7094
3 3GUZ PAF 2.27273
4 1Z8O DEB 2.5641
5 3WCA FPS 3.1339
6 1L8N GCW 3.1339
7 3FYP PEP 3.57143
8 5M7Y MAN MAN MAN 3.7037
9 4ELG 52J 4.21687
10 4XF6 ADP 4.3956
11 4XF6 INS 4.3956
12 4XF6 LIP 4.3956
13 2GQT FAD 4.47761
14 2WQP WQP 4.58453
15 3FQ8 PMP 4.8433
16 5VLQ ANP 4.8433
17 3V66 D3A 5.58824
18 5UXM PEP 5.98291
19 1NVM OXL 6.08696
20 2HV8 GTP 6.39535
21 2BJK NAD 6.55271
22 2D7C GTP 6.58683
23 3K0T BGC 6.99301
24 5O1I 9GH 7.30594
25 1H6H PIB 7.69231
26 2NX1 PEP 8.61423
27 2NX1 RP5 8.61423
28 4BV6 FAD 10.5413
29 1NME 159 13.0137
30 4M6T SAM 13.6612
31 4Z1D PEP 16.3043
32 1RZM PEP 16.568
33 1RZM E4P 16.568
34 4C4P GNP 17.757
35 1M3U KPL 17.803
36 4C1K PEP 24.4275
37 3TFC PEP 27.3504
Pocket No.: 2; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found with APoc: 141
This union binding pocket(no: 2) in the query (biounit: 5cks.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1WN3 HXC None
2 5E9H MLI 1.7094
3 4XCL AGS 1.9305
4 4P6X HCY 1.96078
5 3KFC 61X 1.97628
6 4QS9 BGC 1.9943
7 5NLM IOS 1.9943
8 1XPK HMG 1.9943
9 2Q1H AS4 2
10 4CYI ATP 2.2792
11 5HWO HMG 2.2792
12 3QDC RET 2.51046
13 4YWV SSN 2.5641
14 5EEH SAH 2.5641
15 5EEH P9P 2.5641
16 3WBG 2AN 2.61438
17 1EYQ NAR 2.7027
18 1Q6O LG6 2.77778
19 3RY9 1CA 2.8
20 1D6H COA 2.849
21 6B3A SAM 2.849
22 2Q97 ATP 2.849
23 3RC1 NAP 2.85714
24 3RC1 TLO 2.85714
25 3KC1 2T6 2.96736
26 1NAA 6FA 3.1339
27 5TPR NAD 3.1339
28 4KTP BGC 3.1339
29 4E2J MOF 3.2
30 3GN8 DEX 3.21285
31 5UFS 1TA 3.22581
32 1YYE 196 3.35821
33 5X3R 7Y3 3.41463
34 1YNH SUO 3.4188
35 3H4L ANP 3.4188
36 3WRB GDE 3.4188
37 4NES UDP 3.47594
38 2YAK OSV 3.50877
39 6D28 NEC 3.663
40 5LXT GDP 3.7037
41 5LXT 7AK 3.7037
42 3LDW IPE 3.7037
43 3QFS FAD 3.7037
44 3QFS NAP 3.7037
45 2IO8 ADP 3.7037
46 2ZID GLC GLC GLC 3.7037
47 1GR0 NAD 3.7037
48 1U3R 338 3.73444
49 6ESN BWE 3.74532
50 4J26 EST 3.75
51 4J24 EST 3.75
52 1UU1 PMP HSA 3.8806
53 5MWY YNU 3.93443
54 6CS8 F9Y 3.9604
55 3ICS COA 3.9886
56 4XDU ADP 4.11765
57 3PP0 03Q 4.14201
58 2GFD RDA 4.23729
59 4DXJ IPE 4.2735
60 4DXJ 0M9 4.2735
61 3GD4 FAD 4.2735
62 5GVL PLG 4.2735
63 5GVL GI8 4.2735
64 2VW1 DAN 4.2735
65 5HCV 60R 4.28016
66 3JUQ AJD 4.32432
67 3JUQ AKD 4.32432
68 2PT9 S4M 4.36137
69 5IXK 6EW 4.38596
70 4XF6 LIP 4.3956
71 4XF6 ADP 4.3956
72 4XF6 INS 4.3956
73 4UDB CV7 4.41176
74 5UWA 8ND 4.4335
75 1P7L ANP 4.5584
76 1P7L MET 4.5584
77 2EAE LBT 4.5584
78 1P7L PPK 4.5584
79 1P7L SAM 4.5584
80 4H4D 10E 4.64396
81 4LSJ LSJ 4.65116
82 5UAV TFB 4.65839
83 5QIN J2V 4.74684
84 1YC4 43P 4.92424
85 3KCC CMP 5
86 4R38 RBF 5
87 1M2Z DEX 5.05837
88 3KRL KRL 5.07463
89 3WQQ NDP 5.12821
90 3WQQ IB3 5.12821
91 3V49 PK0 5.26316
92 1Q0H NDP 5.41311
93 4FN4 NAD 5.90551
94 3BEO UD1 5.98291
95 5YJF 8WO 5.98592
96 5YJF SAH 5.98592
97 6B2W AG2 6.00601
98 4N9I PCG 6.19048
99 2OBF F83 6.22837
100 2OBF SAH 6.22837
101 2BII MTV 6.26781
102 1LAF ARG 6.30252
103 4J0M BLD 6.55271
104 5AWQ GLC GLC GLC 6.55271
105 3KRO IPE 6.56934
106 3KRO DST 6.56934
107 1N62 MCN 6.62651
108 5U6C 7YS 6.66667
109 1FFU CDP 6.74847
110 2A92 NAI 6.85358
111 3FS1 MYR 6.95652
112 2HKJ RDC 7.12251
113 2NXW TPP 7.12251
114 1T26 NAI 7.14286
115 1T26 GBD 7.14286
116 5KY3 GFB 7.5
117 5K2M ADP 7.54717
118 3TNF GNP 7.69231
119 5DT6 GLU 7.86517
120 4O1Z MXM 7.97721
121 3HRD MCN 8.125
122 1YKD CMP 8.26211
123 5ETJ IM5 8.64198
124 2XCM ADP 8.69565
125 6C4A PYR 8.83191
126 1QZR ANP 8.83191
127 5CXX FER 9.45455
128 5LX9 OLB 10.5413
129 2QBU SAH 10.7759
130 2QO4 CHD 11.1111
131 1ZXM ANP 11.396
132 6H3O FAD 11.6809
133 3OJI PYV 12.6984
134 5ODQ FAD 13.0435
135 5DJU FMN 13.1148
136 2AIB ERG 13.2653
137 1WDN GLN 14.1593
138 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 15.1515
139 4POJ 2VP 17.7489
140 4M8E 29V 17.7489
141 3H0A 9RA 22.0588
142 1PZL MYR 50
Pocket No.: 3; Query (leader) PDB : 5CKS; Ligand: 52L; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 5cks.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1DTL BEP 3.10559
2 3VSV XYP 4.8433
3 1JH7 UVC 6.34921
4 5XQL C2E 7.56014
Pocket No.: 4; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found with APoc: 81
This union binding pocket(no: 4) in the query (biounit: 5cks.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5UMY TNN 1.42857
2 3SLS ANP 1.64474
3 5EYG NAP 1.88679
4 5B4T 3HR 1.92308
5 5B4T NAD 1.92308
6 1XPM CAA 1.9943
7 2QE4 JJ3 2.01613
8 6B04 C6J 2.05279
9 4KM2 ATR 2.23464
10 4KM2 TOP 2.23464
11 5UC1 486 2.25225
12 3L41 LYS PRO SEP GLN GLU LEU 2.27273
13 3KDU NKS 2.52708
14 4RJK TDL 2.5641
15 1E5Q NDP 2.5641
16 1LC8 33P 2.5641
17 2XVD AS6 2.64901
18 3U2U UDP 2.6616
19 3OJF NDP 2.72374
20 4DK7 0KS 2.83401
21 4PFT MAB 2.849
22 2O1V ADP 2.849
23 2APC UDM 2.92398
24 1DUV PSQ 3.003
25 3WCA FPS 3.1339
26 1JQ5 NAD 3.1339
27 5OJ7 AR6 3.14685
28 1MXH DHF 3.26087
29 4C5N ACP 3.26087
30 1V7C HEY 3.4188
31 2IW1 U2F 3.4188
32 3RYC GTP 3.4965
33 3KF3 FRU 3.7037
34 3LDW ZOL 3.7037
35 3CB2 GDP 3.7037
36 4GBD MCF 3.7037
37 1QG6 NAD 3.83142
38 1QG6 TCL 3.83142
39 4G1V FAD 3.9886
40 3SHR CMP 4.01338
41 4E13 NAD 4.24028
42 5EOU ATP 4.2735
43 4Z87 GDP 4.2735
44 2PT9 2MH 4.36137
45 4MGB XDH 4.70588
46 1RQJ RIS 4.8433
47 4KP7 NAP 5.12821
48 4KP7 1UQ 5.12821
49 3GFZ FMN 5.12821
50 1Y9G FRU 5.12821
51 3K60 ADP 5.38117
52 1Q0H FOM 5.41311
53 4OOE FOM 5.41311
54 2WYA HMG 5.41311
55 1K97 CIR 5.41311
56 1K97 ASP 5.41311
57 4OAR 2S0 5.42636
58 2AX9 BHM 5.46875
59 4P6W MOF 5.55556
60 4U03 GTP 5.69801
61 5JR6 01B PRO PRO ALA NH2 5.98291
62 2IHU TP9 5.98291
63 5TK8 7D5 6.18557
64 1H0H 2MD 6.54206
65 3PDT ADP 6.54545
66 6GAS FAD 6.64653
67 5HZX 2GE 6.81818
68 2Q8M FBP 6.92771
69 5ZGI SIN 7.43802
70 3RJ5 NAD 7.48031
71 3RLF MAL 7.63158
72 3RET PYR 7.92079
73 3RET SAL 7.92079
74 2Z7I 742 7.94118
75 5XPL 8C9 8.48709
76 2AEL SAZ 8.83191
77 5H5O PCG 9.30233
78 3QM1 ZYC 9.43396
79 1T36 ADP 13.9601
80 4IBF 1D5 14.7287
81 5EYP GDP 15.9763
Pocket No.: 5; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5cks.bio1) has 3 residues
No: Leader PDB Ligand Sequence Similarity
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