Receptor
PDB id Resolution Class Description Source Keywords
2d23 1.95 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF EP COMPLEX OF CATALYTIC-SITE MUTANT XYL STREPTOMYCES OLIVACEOVIRIDIS E-86 STREPTOMYCES OLIVACEOVIRIDIS TIM-BARREL RETAINING ENZYME CATALYTIC-SITE MUTANT CHEMICAEP COMPLEX HYDROLASE
Ref.: CRYSTALLOGRAPHIC SNAPSHOTS OF AN ENTIRE REACTION CY RETAINING XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDI J.BIOCHEM. V. 146 61 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1460;
A:1461;
A:1462;
B:960;
B:961;
B:962;
B:963;
B:964;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
XYS AZI XYS D:1;
C:1;
 Valid;
Valid;
 none;
none;
 submit data
307.259 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D24 1.85 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF ES COMPLEX OF CATALYTIC-SITE MUTANT XYL STREPTOMYCES OLIVACEOVIRIDIS E-86 STREPTOMYCES OLIVACEOVIRIDIS TIM-BARREL RETAINING ENZYME CATALYTIC-SITE MUTANT CHEMICAMICHAELIS COMPLEX HYDROLASE
Ref.: CRYSTALLOGRAPHIC SNAPSHOTS OF AN ENTIRE REACTION CY RETAINING XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDI J.BIOCHEM. V. 146 61 2009
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 1ISY - BGC C6 H12 O6 C([C@@H]1[....
2 1V6W - XYP XYP n/a n/a
3 1ISX - XYP XYP n/a n/a
4 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
5 1V6U - XYP XYP n/a n/a
6 1V6X - XYP XYP n/a n/a
7 1V6V - XYP XYP n/a n/a
8 2D24 - XYS XYS n/a n/a
9 2D23 - XYS AZI XYS n/a n/a
10 1IT0 - BGC GAL n/a n/a
11 1ISW - XYP XYP n/a n/a
12 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
13 1ISV - XYP C5 H10 O5 C1[C@H]([C....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 1ISY - BGC C6 H12 O6 C([C@@H]1[....
2 1V6W - XYP XYP n/a n/a
3 1ISX - XYP XYP n/a n/a
4 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
5 1V6U - XYP XYP n/a n/a
6 1V6X - XYP XYP n/a n/a
7 1V6V - XYP XYP n/a n/a
8 2D24 - XYS XYS n/a n/a
9 2D23 - XYS AZI XYS n/a n/a
10 1IT0 - BGC GAL n/a n/a
11 1ISW - XYP XYP n/a n/a
12 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
13 1ISV - XYP C5 H10 O5 C1[C@H]([C....
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1V0M - XDN XYP n/a n/a
2 1V0N - XIF XYP n/a n/a
3 1V0K Ki = 40 uM XYP XDN n/a n/a
4 1V0L Ki = 480 nM XIF XYP n/a n/a
5 1OD8 - XDL XYP n/a n/a
6 3W25 - XYP XYP n/a n/a
7 3W27 - XYS XYP n/a n/a
8 3W26 - XYP XYP XYP n/a n/a
9 3W29 - XYS XYP XYP XYP n/a n/a
10 3W28 - XYS XYP XYP n/a n/a
11 1B30 - XYP XYP XYP n/a n/a
12 1B3V - XYS C5 H10 O5 C1[C@H]([C....
13 1B3Y - XYS C5 H10 O5 C1[C@H]([C....
14 1B3X - XYP XYP XYP n/a n/a
15 1B3Z - XYP XYP XYP n/a n/a
16 1ISY - BGC C6 H12 O6 C([C@@H]1[....
17 1V6W - XYP XYP n/a n/a
18 1ISX - XYP XYP n/a n/a
19 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
20 1V6U - XYP XYP n/a n/a
21 1V6X - XYP XYP n/a n/a
22 1V6V - XYP XYP n/a n/a
23 2D24 - XYS XYS n/a n/a
24 2D23 - XYS AZI XYS n/a n/a
25 1IT0 - BGC GAL n/a n/a
26 1ISW - XYP XYP n/a n/a
27 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
28 1ISV - XYP C5 H10 O5 C1[C@H]([C....
29 3EMZ - HXH C19 H21 N O4 c1ccc(cc1)....
30 3WUE - XYP C5 H10 O5 C1[C@H]([C....
31 3WUG - XYP C5 H10 O5 C1[C@H]([C....
32 1FH7 Ki = 5.8 uM XYP XDN n/a n/a
33 1FHD Ki = 0.15 uM XYP XIM n/a n/a
34 1FH8 Ki = 0.13 uM XYP XIF n/a n/a
35 1J01 Ki = 0.34 uM XIL C10 H17 N O7 C1CNC(=O)[....
36 1FH9 Ki = 0.37 uM LOX XYP n/a n/a
37 5D4Y - XYP XYP n/a n/a
38 2FGL - XYS XYS n/a n/a
39 3NJ3 - XYP XYP n/a n/a
40 1VBR - XYP XYS n/a n/a
41 2BNJ - XYP XYP AHR FER n/a n/a
42 7K4X Kd = 13.04 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
43 5RGA - 6NT C6 H4 N4 O2 c1cc2c(cc1....
44 7K4Z - 6NT C6 H4 N4 O2 c1cc2c(cc1....
45 1GOR - XYS XYP n/a n/a
46 7K4Q Kd = 372.5 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
47 5RGD - 6NT C6 H4 N4 O2 c1cc2c(cc1....
48 7K4U - 6NT C6 H4 N4 O2 c1cc2c(cc1....
49 5RGC - 6NT C6 H4 N4 O2 c1cc2c(cc1....
50 4BS0 Ki = 2 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
51 3NYD - 3NY C6 H4 N4 O2 c1cc2c(cc1....
52 5RGB - 6NT C6 H4 N4 O2 c1cc2c(cc1....
53 5RGE - 6NT C6 H4 N4 O2 c1cc2c(cc1....
54 1GOQ - XYP XYP n/a n/a
55 5RGF - 6NT C6 H4 N4 O2 c1cc2c(cc1....
56 1UQY - XYP XYP XYP XYP n/a n/a
57 1UR1 - XYS XYP AHR n/a n/a
58 1UQZ - XYP XYP XYP GCV n/a n/a
59 3RDK - XYS XYP XYP GCV n/a n/a
60 5OFK - XYP XYP XYP XYP XYP XYP XYP n/a n/a
61 5OFL Ka = 17500 M^-1 BGC BGC BGC BGC BGC BGC n/a n/a
62 1R87 - XYP XYP n/a n/a
63 1HIZ - GLC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: XYS AZI XYS; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 XYS AZI XYS 1 1
2 XYP XYP XYP XYP XYP 0.5 0.653061
3 XYP XYP XYP XYP XYP XYP XYP 0.5 0.653061
4 XYP XYP XYP XYP XYP XYP 0.5 0.653061
5 XYP XYP XYP XYP 0.483333 0.627451
6 XYP XYP 0.464286 0.607843
7 XYP XYP XYP 0.461538 0.64
8 XYP XDN 0.440678 0.642857
9 XYP TRS XYP 0.439394 0.649123
10 XYP XIF 0.416667 0.610169
11 XYS NPO XYS 0.416667 0.683333
Similar Ligands (3D)
Ligand no: 1; Ligand: XYS AZI XYS; Similar ligands found: 100
No: Ligand Similarity coefficient
1 XDL XYP 0.9935
2 XYS XYP 0.9743
3 XIL 0.9651
4 XDN XYP 0.9641
5 LOX XYP 0.9632
6 XYS XYS 0.9568
7 P2L 0.9504
8 XYP XIM 0.9404
9 XIF XYP 0.9376
10 XYP XYS 0.9254
11 WCU 0.9173
12 ISX 0.9163
13 NOC 0.9153
14 27M 0.9126
15 15Q 0.9096
16 AFX 0.9094
17 ARJ 0.9084
18 ADN 0.9069
19 5FD 0.9064
20 LU2 0.9061
21 4KN 0.9048
22 AD3 0.9032
23 TCL 0.9028
24 AJ4 0.9002
25 5CD 0.8980
26 3Q0 0.8976
27 MTA 0.8968
28 5F1 0.8951
29 7VF 0.8942
30 51Y 0.8938
31 NXB 0.8925
32 97K 0.8911
33 8WB 0.8904
34 DFL 0.8903
35 EP4 0.8894
36 AGI 0.8891
37 A45 0.8889
38 2FA 0.8883
39 B4L 0.8876
40 BMC 0.8874
41 6DQ 0.8863
42 Y3J 0.8861
43 OUA 0.8850
44 TGW 0.8848
45 9N2 0.8848
46 7ZO 0.8835
47 XYP AHR 0.8832
48 NAR 0.8828
49 3DH 0.8826
50 KUP 0.8824
51 CWE 0.8816
52 9ME 0.8812
53 4CN 0.8803
54 AJ6 0.8801
55 EZB 0.8794
56 FT1 0.8792
57 4L2 0.8786
58 LI4 0.8782
59 FT2 0.8766
60 QUE 0.8751
61 43F 0.8744
62 OSY 0.8742
63 FY8 0.8736
64 DFV 0.8735
65 MYC 0.8729
66 GQZ 0.8727
67 6QT 0.8726
68 7LU 0.8723
69 FT3 0.8716
70 0NJ 0.8709
71 9ST 0.8695
72 DS8 0.8686
73 M16 0.8685
74 4YE 0.8679
75 08C 0.8679
76 NPZ 0.8663
77 CHV 0.8655
78 YUG 0.8654
79 CIW 0.8647
80 GF7 0.8645
81 GAL PHB 0.8643
82 SAK 0.8641
83 9MK 0.8635
84 1Q1 0.8631
85 CC6 0.8625
86 C4F 0.8621
87 6BK 0.8619
88 B72 0.8612
89 IMV 0.8607
90 E2N 0.8607
91 LI7 0.8591
92 CMP 0.8590
93 9M9 0.8581
94 AMP 0.8571
95 121 0.8571
96 NU3 0.8562
97 DMB 0.8543
98 147 0.8543
99 FB4 0.8541
100 A63 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D24; Ligand: XYS XYS XYS XYS XYS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2d24.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2D24; Ligand: XYS XYS; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 2d24.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3AJ6 NGA 6.29371
2 3AJ6 NGA 6.29371
3 2ZQO NGA 6.92308
4 2ZQO NGA 6.92308
5 2ZQO NGA 6.92308
6 2ZQO NGA 6.92308
7 5MUA GAL 16.4336
8 5MUA GAL 16.4336
9 4OUJ GLC GAL 16.9381
10 4OUJ GLC GAL 16.9381
11 4ZGR NGA GAL 18.7739
12 4LO2 BGC GAL 19.7279
13 4LO2 BGC GAL 19.7279
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