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 5 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: 141
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL 1 1
2 BMA 1 1
3 GXL 1 1
4 GLA 1 1
5 ALL 1 1
6 GLC 1 1
7 BGC 1 1
8 GIV 1 1
9 MAN 1 1
10 WOO 1 1
11 32O 0.653846 0.866667
12 RIB 0.653846 0.866667
13 FUB 0.653846 0.866667
14 Z6J 0.653846 0.866667
15 AHR 0.653846 0.866667
16 BMA BMA MAN 0.545455 0.823529
17 GLA BGC 0.511628 0.848485
18 LAK 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 GLA GLC 0.511628 0.848485
23 GAL GAL 0.511628 0.848485
24 MLB 0.511628 0.848485
25 BMA GLA 0.511628 0.848485
26 BMA BMA BMA BMA BMA BMA MAN 0.5 0.823529
27 YDR 0.5 0.8
28 MAN BMA BMA BMA BMA BMA 0.5 0.823529
29 GLC GLC GLC GLC BGC 0.488889 0.848485
30 GLC GLC GLC 0.488889 0.848485
31 MAN MAN MAN 0.488889 0.848485
32 GLC GLC GLC GLC GLC BGC 0.488889 0.848485
33 BGP 0.461538 0.675
34 G6P 0.461538 0.675
35 M6P 0.461538 0.675
36 A6P 0.461538 0.675
37 M6D 0.461538 0.675
38 BG6 0.461538 0.675
39 SHG 0.457143 0.875
40 GAF 0.457143 0.875
41 G2F 0.457143 0.875
42 X6X 0.457143 0.777778
43 2FG 0.457143 0.875
44 G3F 0.457143 0.875
45 PA1 0.457143 0.777778
46 1GN 0.457143 0.777778
47 GCS 0.457143 0.777778
48 2H5 0.457143 0.875
49 LB2 0.454545 0.848485
50 BGC BMA 0.454545 0.848485
51 BGC GAL 0.454545 0.848485
52 MAL 0.454545 0.848485
53 GLC GAL 0.454545 0.848485
54 M3M 0.454545 0.848485
55 GLA GAL 0.454545 0.848485
56 MAB 0.454545 0.848485
57 GLC BGC 0.454545 0.848485
58 BMA BMA 0.454545 0.848485
59 LBT 0.454545 0.848485
60 MAL MAL 0.454545 0.823529
61 CBK 0.454545 0.848485
62 GLA GLA 0.454545 0.848485
63 MAN GLC 0.454545 0.848485
64 CBI 0.454545 0.848485
65 N9S 0.454545 0.848485
66 GAL GLC 0.454545 0.848485
67 BMA GAL 0.454545 0.848485
68 B2G 0.454545 0.848485
69 BGC GLC 0.454545 0.848485
70 LAT 0.454545 0.848485
71 GAL BGC 0.454545 0.848485
72 3MG 0.444444 0.875
73 TCB 0.444444 0.8
74 GLC SGC 0.444444 0.8
75 YIO 0.441176 0.870968
76 2GS 0.432432 0.875
77 BGC BGC 0.431818 0.848485
78 2M4 0.431818 0.848485
79 MAN MAN 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 CT3 0.416667 0.848485
84 GLC BGC GLC 0.416667 0.848485
85 MLR 0.416667 0.848485
86 GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
87 GLC GLC GLC GLC GLC 0.416667 0.848485
88 GAL FUC 0.416667 0.848485
89 BMA BMA BMA 0.416667 0.848485
90 CTR 0.416667 0.848485
91 BGC GLC GLC 0.416667 0.848485
92 BGC GLC GLC GLC GLC 0.416667 0.848485
93 MAN MAN BMA BMA BMA BMA 0.416667 0.848485
94 GLC GAL GAL 0.416667 0.848485
95 B4G 0.416667 0.848485
96 CEX 0.416667 0.848485
97 MAN BMA BMA BMA BMA 0.416667 0.848485
98 BMA BMA BMA BMA BMA 0.416667 0.848485
99 GLC BGC BGC BGC BGC BGC 0.416667 0.848485
100 CTT 0.416667 0.848485
101 GLC GLC BGC 0.416667 0.848485
102 DXI 0.416667 0.848485
103 GLC GLC BGC GLC GLC GLC GLC 0.416667 0.848485
104 BGC GLC GLC GLC 0.416667 0.848485
105 BGC BGC BGC GLC 0.416667 0.848485
106 BGC BGC BGC BGC BGC BGC 0.416667 0.848485
107 BMA BMA BMA BMA BMA BMA 0.416667 0.848485
108 MTT 0.416667 0.848485
109 BMA MAN BMA 0.416667 0.848485
110 BGC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
111 CE5 0.416667 0.848485
112 GAL GAL GAL 0.416667 0.848485
113 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.848485
114 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
115 GLA GAL GLC 0.416667 0.848485
116 CE6 0.416667 0.848485
117 GLC BGC BGC BGC BGC 0.416667 0.848485
118 GLC BGC BGC 0.416667 0.848485
119 MAN BMA BMA 0.416667 0.848485
120 MT7 0.416667 0.848485
121 GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
122 CE8 0.416667 0.848485
123 CEY 0.416667 0.848485
124 BGC BGC BGC 0.408163 0.848485
125 BGC BGC BGC BGC BGC 0.408163 0.848485
126 GLC BGC BGC BGC BGC BGC BGC 0.408163 0.848485
127 SGC SGC BGC 0.408163 0.8
128 GLC BGC BGC BGC 0.408163 0.848485
129 BGC BGC BGC ASO BGC BGC ASO 0.408163 0.848485
130 BGC BGC BGC GLC BGC BGC 0.408163 0.848485
131 TRE 0.405405 0.848485
132 1LL 0.405405 0.771429
133 TDG 0.405405 0.771429
134 BM3 0.404762 0.7
135 NDG 0.404762 0.7
136 NAG 0.404762 0.7
137 HSQ 0.404762 0.7
138 A2G 0.404762 0.7
139 NGA 0.404762 0.7
140 FUB AHR AHR 0.4 0.764706
141 AHR AHR AHR 0.4 0.764706
Ligand no: 2; Ligand: 52L; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 52L 1 1
2 LXP 0.511628 0.680851
3 DX5 0.511628 0.680851
4 A5P 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 LG6 0.479167 0.755556
10 6PG 0.479167 0.755556
11 DG6 0.478261 0.666667
12 I22 0.46 0.702128
13 TG6 0.44898 0.702128
14 F6R 0.44898 0.702128
15 TX4 0.446809 0.745098
16 LX1 0.444444 0.659574
17 DEZ 0.434783 0.755556
18 S6P 0.434783 0.659574
19 DER 0.434783 0.755556
20 PAN 0.431373 0.784314
21 P6T 0.431373 0.717391
22 P6F 0.431373 0.717391
23 2FP 0.431373 0.717391
24 R5P 0.416667 0.733333
25 R52 0.416667 0.733333
26 4TP 0.416667 0.791667
27 5RP 0.408163 0.723404
28 HMS 0.408163 0.723404
29 5SP 0.408163 0.723404
30 HG3 0.404762 0.666667
31 G6Q 0.4 0.733333
32 M6R 0.4 0.72
33 AGP 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: 14
This union binding pocket(no: 1) in the query (biounit: 5cks.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Z8O DEB 0.006914 0.42688 2.5641
2 3WCA FPS 0.0172 0.40752 3.1339
3 3FYP PEP 0.00006515 0.47042 3.57143
4 5M7Y MAN MAN MAN 0.01129 0.40339 3.7037
5 2GQT FAD 0.04023 0.41139 4.47761
6 3FQ8 PMP 0.009052 0.41669 4.8433
7 2D7C GTP 0.01813 0.40359 6.58683
8 1H6H PIB 0.02378 0.40102 7.69231
9 2NX1 PEP 0.0008425 0.50448 8.61423
10 2NX1 RP5 0.0009781 0.50106 8.61423
11 4BV6 FAD 0.04686 0.40032 10.5413
12 4Z1D PEP 0.0000009851 0.51768 16.3043
13 1M3U KPL 0.01285 0.40268 17.803
14 4C1K PEP 0.00005406 0.52946 24.4275
Pocket No.: 2; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found: 38
This union binding pocket(no: 2) in the query (biounit: 5cks.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4P6X HCY 0.009516 0.42219 1.96078
2 3KFC 61X 0.04776 0.40449 1.97628
3 1XPK HMG 0.04416 0.40238 1.9943
4 2Q97 ATP 0.03123 0.40096 2.849
5 3GN8 DEX 0.01287 0.41544 3.21285
6 1YYE 196 0.01554 0.40446 3.35821
7 1YNH SUO 0.01692 0.41124 3.4188
8 3QFS FAD 0.03416 0.41361 3.7037
9 3QFS NAP 0.03416 0.41361 3.7037
10 2ZID GLC GLC GLC 0.01703 0.40305 3.7037
11 4J26 EST 0.005371 0.42316 3.75
12 4J24 EST 0.008678 0.40882 3.75
13 3ICS COA 0.03365 0.413 3.9886
14 4DXJ IPE 0.01443 0.42951 4.2735
15 4DXJ 0M9 0.01962 0.42106 4.2735
16 5GVL GI8 0.03124 0.40881 4.2735
17 5GVL PLG 0.03124 0.40881 4.2735
18 2VW1 DAN 0.02587 0.40757 4.2735
19 2PT9 S4M 0.03586 0.40122 4.36137
20 4LSJ LSJ 0.0126 0.415 4.65116
21 4R38 RBF 0.02152 0.41255 5
22 3WQQ NDP 0.04121 0.41373 5.12821
23 3WQQ IB3 0.04121 0.41373 5.12821
24 3V49 PK0 0.009104 0.43192 5.26316
25 1LAF ARG 0.01514 0.41653 6.30252
26 4J0M BLD 0.02059 0.40321 6.55271
27 3KRO IPE 0.02783 0.40821 6.56934
28 3KRO DST 0.02783 0.40821 6.56934
29 1N62 MCN 0.008478 0.45026 6.62651
30 3FS1 MYR 0.005742 0.42558 6.95652
31 5KY3 GFB 0.02282 0.40513 7.5
32 5DT6 GLU 0.01561 0.40032 7.86517
33 5ETJ IM5 0.02442 0.40254 8.64198
34 2XCM ADP 0.00284 0.44439 8.69565
35 3OJI PYV 0.0172 0.41151 12.6984
36 2AIB ERG 0.0278 0.40303 13.2653
37 4M8E 29V 0.01096 0.4192 17.7489
38 3H0A 9RA 0.01076 0.41843 22.0588
39 1PZL MYR 0.005409 0.43026 50
Pocket No.: 3; Query (leader) PDB : 5CKS; Ligand: 52L; 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: 5cks.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5cks.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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