Receptor
PDB id Resolution Class Description Source Keywords
1XYC 2.19 Å EC: 5.3.1.5 X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBS COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR MM OVEMENT DURING CATALYSIS STREPTOMYCES OLIVOCHROMOGENES ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Ref.: X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRAT PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSI BIOCHEMISTRY V. 33 5469 1994
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3MF A:950;
B:960;
Valid;
Valid;
none;
none;
submit data
194.182 C7 H14 O6 CO[C@...
MG A:400;
A:401;
B:900;
B:901;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GYI 1.6 Å EC: 5.3.1.5 DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE I INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-C RYSTALLOGRAPHIC STRUCTURE OF THE ENZYME-INHIBITOR COMPLEX STREPTOMYCES OLIVOCHROMOGENES ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Ref.: DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT ISOMERASE INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHIC STRUCTURE OF ENZYME-INHIBITOR COMPLEX BIOCHEMISTRY V. 34 3742 1995
Members (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1S5M - GLC C6 H12 O6 C([C@@H]1[....
2 3KBM - GLC C6 H12 O6 C([C@@H]1[....
3 4QEH - 32O C5 H10 O5 C([C@H]1[C....
4 3U3H - 03W C3 H8 O4 C([C@H](C(....
5 1XID - ASC C6 H8 O6 C([C@@H]([....
6 4DUO - XYL C5 H12 O5 C([C@@H](C....
7 4QE5 - RUU C5 H10 O5 C1[C@@H]([....
8 6RNF - GLC C6 H12 O6 C([C@@H]1[....
9 1XIH - SOR C6 H14 O6 C([C@@H]([....
10 4ZBC - GLC C6 H12 O6 C([C@@H]1[....
11 4QEE - Z6J C5 H10 O5 C([C@H]1[C....
12 1XIG - XYL C5 H12 O5 C([C@@H](C....
13 1XYC - 3MF C7 H14 O6 CO[C@@H]([....
14 5ZYE - GLC C6 H12 O6 C([C@@H]1[....
15 2XIS - XYL C5 H12 O5 C([C@@H](C....
16 1XYM - GLO C6 H12 O6 C([C@H]([C....
17 8XIA - XLS C5 H10 O5 C([C@H]([C....
18 1XIJ - THE C4 H7 O5 C([C@H]([C....
19 4XIS - XLS C5 H10 O5 C([C@H]([C....
20 1GW9 - LXC C5 H10 O5 C1[C@@H]([....
21 1XIC - XLS C5 H10 O5 C([C@H]([C....
22 1XII - XUL C5 H10 O5 C([C@H]([C....
23 6QNI - GLC C6 H12 O6 C([C@@H]1[....
24 4ZB5 - GLC C6 H12 O6 C([C@@H]1[....
25 1XYB - GLO C6 H12 O6 C([C@H]([C....
26 4ZB2 - FRU C6 H12 O6 C([C@@H]1[....
27 6QNJ - GLC C6 H12 O6 C([C@@H]1[....
28 4QE4 - 34V C5 H10 O5 C1[C@@H]([....
29 4ZB0 - GLC C6 H12 O6 C([C@@H]1[....
30 2GYI Ki < 100 nM HYA C4 H9 N O5 C([C@H]([C....
31 4QE1 - RUU C5 H10 O5 C1[C@@H]([....
32 6RND - GLC C6 H12 O6 C([C@@H]1[....
33 1S5N - XYL C5 H12 O5 C([C@@H](C....
34 1XIF - GLC C6 H12 O6 C([C@@H]1[....
35 3XIS - XLS C5 H10 O5 C([C@H]([C....
36 6QND - GLO C6 H12 O6 C([C@H]([C....
37 1XIE - ASO C6 H12 O5 C1[C@@H]([....
38 3KBN - GLO C6 H12 O6 C([C@H]([C....
39 6QNC - GLC C6 H12 O6 C([C@@H]1[....
70% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1S5M - GLC C6 H12 O6 C([C@@H]1[....
2 3KBM - GLC C6 H12 O6 C([C@@H]1[....
3 4QEH - 32O C5 H10 O5 C([C@H]1[C....
4 3U3H - 03W C3 H8 O4 C([C@H](C(....
5 1XID - ASC C6 H8 O6 C([C@@H]([....
6 4DUO - XYL C5 H12 O5 C([C@@H](C....
7 4QE5 - RUU C5 H10 O5 C1[C@@H]([....
8 6RNF - GLC C6 H12 O6 C([C@@H]1[....
9 1XIH - SOR C6 H14 O6 C([C@@H]([....
10 4ZBC - GLC C6 H12 O6 C([C@@H]1[....
11 4QEE - Z6J C5 H10 O5 C([C@H]1[C....
12 1XIG - XYL C5 H12 O5 C([C@@H](C....
13 1XYC - 3MF C7 H14 O6 CO[C@@H]([....
14 5ZYE - GLC C6 H12 O6 C([C@@H]1[....
15 2XIS - XYL C5 H12 O5 C([C@@H](C....
16 1XYM - GLO C6 H12 O6 C([C@H]([C....
17 8XIA - XLS C5 H10 O5 C([C@H]([C....
18 1XIJ - THE C4 H7 O5 C([C@H]([C....
19 4XIS - XLS C5 H10 O5 C([C@H]([C....
20 1GW9 - LXC C5 H10 O5 C1[C@@H]([....
21 1XIC - XLS C5 H10 O5 C([C@H]([C....
22 1XII - XUL C5 H10 O5 C([C@H]([C....
23 6QNI - GLC C6 H12 O6 C([C@@H]1[....
24 4ZB5 - GLC C6 H12 O6 C([C@@H]1[....
25 1XYB - GLO C6 H12 O6 C([C@H]([C....
26 4ZB2 - FRU C6 H12 O6 C([C@@H]1[....
27 6QNJ - GLC C6 H12 O6 C([C@@H]1[....
28 4QE4 - 34V C5 H10 O5 C1[C@@H]([....
29 4ZB0 - GLC C6 H12 O6 C([C@@H]1[....
30 2GYI Ki < 100 nM HYA C4 H9 N O5 C([C@H]([C....
31 4QE1 - RUU C5 H10 O5 C1[C@@H]([....
32 6RND - GLC C6 H12 O6 C([C@@H]1[....
33 1S5N - XYL C5 H12 O5 C([C@@H](C....
34 1XIF - GLC C6 H12 O6 C([C@@H]1[....
35 3XIS - XLS C5 H10 O5 C([C@H]([C....
36 6QND - GLO C6 H12 O6 C([C@H]([C....
37 1XIE - ASO C6 H12 O5 C1[C@@H]([....
38 3KBN - GLO C6 H12 O6 C([C@H]([C....
39 6QNC - GLC C6 H12 O6 C([C@@H]1[....
40 1DID - DIG C6 H13 N O4 C([C@H]1[C....
41 1XLC - XYL C5 H12 O5 C([C@@H](C....
42 1XLJ - XYL C5 H12 O5 C([C@@H](C....
43 1DIE - NOJ C6 H13 N O4 C1[C@@H]([....
44 1XLF - GCO C6 H12 O7 C([C@H]([C....
45 4XIA - SOR C6 H14 O6 C([C@@H]([....
46 1XLM - XYL C5 H12 O5 C([C@@H](C....
47 5XIA - XYL C5 H12 O5 C([C@@H](C....
48 1XLI Ki = 33 mM GLT C6 H12 O5 S C([C@@H]1[....
49 1XLG - XYL C5 H12 O5 C([C@@H](C....
50 1XLD - XYL C5 H12 O5 C([C@@H](C....
51 2XIN - SOR C6 H14 O6 C([C@@H]([....
52 8XIM - XLS C5 H10 O5 C([C@H]([C....
53 1XIM - XYL C5 H12 O5 C([C@@H](C....
54 2XIM - XYL C5 H12 O5 C([C@@H](C....
55 1XIN - XYL C5 H12 O5 C([C@@H](C....
56 3XIM - SOR C6 H14 O6 C([C@@H]([....
57 5XIN - XLS C5 H10 O5 C([C@H]([C....
58 9XIM - XLS C5 H10 O5 C([C@H]([C....
59 6XIM - XLS C5 H10 O5 C([C@H]([C....
50% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1S5M - GLC C6 H12 O6 C([C@@H]1[....
2 3KBM - GLC C6 H12 O6 C([C@@H]1[....
3 4QEH - 32O C5 H10 O5 C([C@H]1[C....
4 3U3H - 03W C3 H8 O4 C([C@H](C(....
5 1XID - ASC C6 H8 O6 C([C@@H]([....
6 4DUO - XYL C5 H12 O5 C([C@@H](C....
7 4QE5 - RUU C5 H10 O5 C1[C@@H]([....
8 6RNF - GLC C6 H12 O6 C([C@@H]1[....
9 1XIH - SOR C6 H14 O6 C([C@@H]([....
10 4ZBC - GLC C6 H12 O6 C([C@@H]1[....
11 4QEE - Z6J C5 H10 O5 C([C@H]1[C....
12 1XIG - XYL C5 H12 O5 C([C@@H](C....
13 1XYC - 3MF C7 H14 O6 CO[C@@H]([....
14 5ZYE - GLC C6 H12 O6 C([C@@H]1[....
15 2XIS - XYL C5 H12 O5 C([C@@H](C....
16 1XYM - GLO C6 H12 O6 C([C@H]([C....
17 8XIA - XLS C5 H10 O5 C([C@H]([C....
18 1XIJ - THE C4 H7 O5 C([C@H]([C....
19 4XIS - XLS C5 H10 O5 C([C@H]([C....
20 1GW9 - LXC C5 H10 O5 C1[C@@H]([....
21 1XIC - XLS C5 H10 O5 C([C@H]([C....
22 1XII - XUL C5 H10 O5 C([C@H]([C....
23 6QNI - GLC C6 H12 O6 C([C@@H]1[....
24 4ZB5 - GLC C6 H12 O6 C([C@@H]1[....
25 1XYB - GLO C6 H12 O6 C([C@H]([C....
26 4ZB2 - FRU C6 H12 O6 C([C@@H]1[....
27 6QNJ - GLC C6 H12 O6 C([C@@H]1[....
28 4QE4 - 34V C5 H10 O5 C1[C@@H]([....
29 4ZB0 - GLC C6 H12 O6 C([C@@H]1[....
30 2GYI Ki < 100 nM HYA C4 H9 N O5 C([C@H]([C....
31 4QE1 - RUU C5 H10 O5 C1[C@@H]([....
32 6RND - GLC C6 H12 O6 C([C@@H]1[....
33 1S5N - XYL C5 H12 O5 C([C@@H](C....
34 1XIF - GLC C6 H12 O6 C([C@@H]1[....
35 3XIS - XLS C5 H10 O5 C([C@H]([C....
36 6QND - GLO C6 H12 O6 C([C@H]([C....
37 1XIE - ASO C6 H12 O5 C1[C@@H]([....
38 3KBN - GLO C6 H12 O6 C([C@H]([C....
39 6QNC - GLC C6 H12 O6 C([C@@H]1[....
40 1DID - DIG C6 H13 N O4 C([C@H]1[C....
41 1XLC - XYL C5 H12 O5 C([C@@H](C....
42 1XLJ - XYL C5 H12 O5 C([C@@H](C....
43 1DIE - NOJ C6 H13 N O4 C1[C@@H]([....
44 1XLF - GCO C6 H12 O7 C([C@H]([C....
45 4XIA - SOR C6 H14 O6 C([C@@H]([....
46 1XLM - XYL C5 H12 O5 C([C@@H](C....
47 5XIA - XYL C5 H12 O5 C([C@@H](C....
48 1XLI Ki = 33 mM GLT C6 H12 O5 S C([C@@H]1[....
49 1XLG - XYL C5 H12 O5 C([C@@H](C....
50 1XLD - XYL C5 H12 O5 C([C@@H](C....
51 2XIN - SOR C6 H14 O6 C([C@@H]([....
52 8XIM - XLS C5 H10 O5 C([C@H]([C....
53 1XIM - XYL C5 H12 O5 C([C@@H](C....
54 2XIM - XYL C5 H12 O5 C([C@@H](C....
55 1XIN - XYL C5 H12 O5 C([C@@H](C....
56 3XIM - SOR C6 H14 O6 C([C@@H]([....
57 5XIN - XLS C5 H10 O5 C([C@H]([C....
58 9XIM - XLS C5 H10 O5 C([C@H]([C....
59 6XIM - XLS C5 H10 O5 C([C@H]([C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 3MF; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 3MF 1 1
2 SOL 0.432432 0.846154
3 TAG 0.432432 0.846154
4 LPK 0.432432 0.846154
5 SDD 0.432432 0.846154
6 FUD 0.432432 0.846154
7 PSJ 0.432432 0.846154
Similar Ligands (3D)
Ligand no: 1; Ligand: 3MF; Similar ligands found: 150
No: Ligand Similarity coefficient
1 GLO 0.9514
2 SOR 0.9468
3 CS2 0.9409
4 3BU 0.9322
5 MTL 0.9311
6 FIX 0.9228
7 GCO 0.9147
8 REL 0.9139
9 LFC 0.9093
10 M72 0.9066
11 CCB 0.9049
12 4A5 0.9047
13 4VY 0.9042
14 2AS 0.9032
15 TAR 0.9013
16 MLE 0.9011
17 XYL 0.8996
18 AL0 0.8994
19 ICT 0.8988
20 XYH 0.8986
21 RAT 0.8972
22 CIT 0.8962
23 GLY ASP 0.8947
24 GBN 0.8943
25 KDG 0.8939
26 TRC 0.8934
27 FLC 0.8932
28 AOS 0.8921
29 M74 0.8908
30 LLH 0.8906
31 2C0 0.8902
32 0QW 0.8901
33 HHT 0.8898
34 DAL DAL 0.8895
35 NCD 0.8895
36 2AL 0.8895
37 GZQ 0.8893
38 GLY LEU 0.8887
39 GLY CYS 0.8880
40 QUS 0.8880
41 NCT 0.8876
42 TT4 0.8866
43 XUL 0.8862
44 5UK 0.8860
45 2ED 0.8858
46 2CG 0.8857
47 XQB 0.8844
48 X8Z 0.8843
49 56D 0.8841
50 HDL 0.8828
51 7A2 0.8822
52 ALA LEU 0.8822
53 GLR 0.8814
54 1L5 0.8813
55 Q07 0.8813
56 GVG 0.8813
57 AOR 0.8812
58 41K 0.8810
59 GRO 0.8809
60 HHH 0.8807
61 GLN 0.8800
62 LNO 0.8799
63 AN0 0.8789
64 40F 0.8789
65 256 0.8788
66 TYE 0.8786
67 46P 0.8786
68 RNS 0.8783
69 8WQ 0.8772
70 GLU 0.8769
71 HL4 0.8764
72 P4B 0.8761
73 3CR 0.8761
74 QIC 0.8761
75 4WK 0.8755
76 DEE 0.8753
77 5FX 0.8750
78 HNK 0.8745
79 RNT 0.8743
80 KMH 0.8734
81 S2T 0.8733
82 ZZI 0.8733
83 A29 0.8732
84 23J 0.8727
85 LNR 0.8715
86 TRP 0.8713
87 2F6 0.8710
88 87L 0.8705
89 RMN 0.8704
90 Z5P 0.8704
91 173 0.8702
92 HQJ 0.8697
93 B09 0.8696
94 HYA 0.8696
95 CUW 0.8694
96 6JN 0.8691
97 9SE 0.8683
98 FOC 0.8681
99 3MV 0.8678
100 NLG 0.8678
101 49O 0.8677
102 SQV 0.8677
103 0FA 0.8677
104 C4L 0.8675
105 E1P 0.8667
106 791 0.8666
107 I38 0.8665
108 RB5 0.8664
109 DXG 0.8663
110 NZ2 0.8659
111 ONR 0.8659
112 SKJ 0.8658
113 FF3 0.8651
114 ALA ALA 0.8649
115 M5E 0.8645
116 1WC 0.8641
117 BZQ 0.8637
118 AQK 0.8634
119 HJ7 0.8627
120 CFA 0.8627
121 FEH 0.8625
122 HCT 0.8623
123 F69 0.8622
124 GLY MET 0.8620
125 DEW 0.8612
126 6DP 0.8611
127 S2P 0.8607
128 TPO 0.8606
129 SAF 0.8605
130 7QD 0.8604
131 5ZZ 0.8604
132 7A3 0.8599
133 3TC 0.8592
134 MIC 0.8587
135 7UC 0.8581
136 E4P 0.8579
137 SDF 0.8577
138 6TZ 0.8569
139 OSE 0.8566
140 4HP 0.8557
141 KJM 0.8551
142 NFQ 0.8550
143 ONL 0.8544
144 SHI 0.8541
145 SYM 0.8540
146 5XB 0.8536
147 L13 0.8532
148 RBL 0.8529
149 ENO 0.8520
150 T2D 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GYI; Ligand: HYA; Similar sites found with APoc: 6
This union binding pocket(no: 1) in the query (biounit: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
1 1DE6 RNS 7.51295
2 1DE6 RNS 7.51295
3 1DE6 RNS 7.51295
4 1DE6 RNS 7.51295
5 2I56 RNS 10.8808
6 2I56 RNS 10.8808
Pocket No.: 2; Query (leader) PDB : 2GYI; Ligand: HYA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2GYI; Ligand: HYA; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
1 1DE6 RNS 7.51295
2 1DE6 RNS 7.51295
3 1DE6 RNS 7.51295
4 1DE6 RNS 7.51295
5 2I56 RNS 10.8808
6 2I56 RNS 10.8808
Pocket No.: 4; Query (leader) PDB : 2GYI; Ligand: HYA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
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