Receptor
PDB id Resolution Class Description Source Keywords
1RRV 2 Å EC: 2.-.-.- X-RAY CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEX WITH TDP AND THE NATURAL SUBSTRATE, DESVANCOSAMINYLV ANCOMYCIN. AMYCOLATOPSIS ORIENTALIS GT-B GLYCOSYLTRANSFERASE ROSSMANN FOLD GLYCOPEPTIDE VACOANTIBIOTIC TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: CRYSTAL STRUCTURE OF VANCOSAMINYLTRANSFERASE GTFD F VANCOMYCIN BIOSYNTHETIC PATHWAY: INTERACTIONS WITH AND NUCLEOTIDE LIGANDS BIOCHEMISTRY V. 43 5170 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1005;
A:1006;
B:1007;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
K A:417;
B:417;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
MLU OMZ ASN GHP GHP OMY 3FG BGC C:1;
D:1;
Valid;
Valid;
none;
none;
submit data
1306.08 n/a Clc1c...
TYD A:1003;
B:1004;
Valid;
Valid;
none;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RRV 2 Å EC: 2.-.-.- X-RAY CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEX WITH TDP AND THE NATURAL SUBSTRATE, DESVANCOSAMINYLV ANCOMYCIN. AMYCOLATOPSIS ORIENTALIS GT-B GLYCOSYLTRANSFERASE ROSSMANN FOLD GLYCOPEPTIDE VACOANTIBIOTIC TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: CRYSTAL STRUCTURE OF VANCOSAMINYLTRANSFERASE GTFD F VANCOMYCIN BIOSYNTHETIC PATHWAY: INTERACTIONS WITH AND NUCLEOTIDE LIGANDS BIOCHEMISTRY V. 43 5170 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 1RRV - MLU OMZ ASN GHP GHP OMY 3FG BGC n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 1RRV - MLU OMZ ASN GHP GHP OMY 3FG BGC n/a n/a
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3H4I - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
2 3H4T - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 1RRV - MLU OMZ ASN GHP GHP OMY 3FG BGC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MLU OMZ ASN GHP GHP OMY 3FG BGC; Similar ligands found: 6
Ligand no: 2; Ligand: TYD; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 TYD 1 1
2 TTP 0.884058 1
3 TMP 0.80597 0.985714
4 TLO 0.716049 0.945205
5 DAU 0.694118 0.932432
6 18T 0.682353 0.932432
7 TDX 0.682353 0.945205
8 3R2 0.682353 0.92
9 1JB 0.682353 0.932432
10 TRH 0.682353 0.932432
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3F 0.666667 0.907895
15 T3Q 0.666667 0.907895
16 TBD 0.662338 0.958904
17 0N2 0.659091 0.896104
18 T46 0.659091 0.932432
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 LLT 0.641791 0.873239
23 THM 0.641791 0.873239
24 QDM 0.637363 0.896104
25 AKM 0.630435 0.886076
26 FNF 0.630435 0.92
27 JHZ 0.630435 0.884615
28 1YF 0.630435 0.92
29 4TG 0.623656 0.92
30 DUD 0.61039 0.957143
31 0DN 0.6 0.833333
32 UFP 0.6 0.905405
33 DT DT DT DT DT 0.582418 0.945205
34 QUH 0.58 0.907895
35 FUH 0.58 0.907895
36 T5A 0.572816 0.841463
37 5HU 0.571429 0.971831
38 BRU 0.571429 0.905405
39 FDM 0.564103 0.918919
40 NYM 0.564103 0.958333
41 5IU 0.564103 0.905405
42 DT DT PST 0.56383 0.881579
43 T3P 0.56 0.943662
44 THP 0.556962 0.971429
45 ATM 0.542169 0.894737
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 TXS 0.538462 0.789474
49 YYY 0.536585 0.891892
50 T3S 0.525 0.789474
51 BVP 0.52381 0.944444
52 ABT 0.521739 0.884615
53 DT DT DT 0.511364 0.878378
54 D4D 0.506024 0.928571
55 7SG 0.504274 0.864198
56 TQP 0.504274 0.864198
57 T5K 0.5 0.853659
58 TPE 0.5 0.894737
59 DT ME6 DT 0.5 0.87013
60 T4K 0.5 0.853659
61 2DT 0.5 0.957747
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 AZZ 0.469136 0.779221
66 UMP 0.469136 0.942857
67 DU 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 D4T 0.449438 0.928571
71 DUP 0.449438 0.930556
72 6U4 0.447917 0.848101
73 DDN 0.439024 0.942857
74 3DT 0.428571 0.835616
75 UC5 0.425287 0.943662
76 ID2 0.423077 0.8
77 DT MA7 DT 0.420635 0.797619
78 8DG 0.418367 0.829268
79 DUN 0.41573 0.930556
80 DUT MG 0.413043 0.864865
81 5GW 0.410526 0.878378
82 DC 0.406977 0.878378
83 DCM 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 ADS THS THS THS 0.403361 0.767442
86 74W 0.4 0.732558
87 D4M 0.4 0.914286
88 74X 0.4 0.732558
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RRV; Ligand: TYD; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 1rrv.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4X1T UDP 0.0002258 0.4607 1.22549
2 2ZWA SAH 0.008286 0.40567 1.68269
3 2VCH UDP 0.0003061 0.47875 1.92308
4 4XSU GLC 0.01109 0.40459 2.06186
5 4XSU UDP 0.01109 0.40459 2.06186
6 1HV9 UD1 0.008403 0.41424 2.16346
7 1RM0 D6P 0.03876 0.40101 2.16346
8 3Q9T FAY 0.02428 0.40262 2.64423
9 3EYA TDP 0.007891 0.41131 3.125
10 2C1X UDP 0.002748 0.44549 3.36538
11 5GVR LMR 0.02757 0.40708 3.4188
12 3HBN UDP 0.003104 0.41707 3.5461
13 5V2J 7WV 0.0001852 0.49356 4.56731
14 5V2J UDP 0.0001852 0.49356 4.56731
15 1QO8 FAD 0.01691 0.41386 4.80769
16 5TME UDP 0.00006328 0.51537 5.28846
17 3HBF UDP 0.0007385 0.44862 5.28846
18 3HBF MYC 0.002227 0.44741 5.28846
19 4GYW UDP 0.01454 0.4069 5.28846
20 5BNW 12V 0.0191 0.40247 5.28846
21 1T36 ADP 0.01488 0.40015 6.49038
22 5G41 AP5 0.02324 0.40801 6.72646
23 3S2U UD1 0.0006196 0.45404 6.84932
24 3OTI TYD 0.00001459 0.52631 7.03518
25 2VBU CDP 0.0204 0.4 7.35294
26 4PQG UDP 0.001835 0.414 7.45192
27 1D4D FAD 0.01055 0.42465 8.89423
28 3IAA TYD 0.00001816 0.51964 9.61539
29 3RSC TYD 0.00001509 0.52565 9.63855
30 1KOL NAD 0.01999 0.40471 10.3015
31 2IYF UDP 0.0004946 0.44714 10.5769
32 3UYK 0CX 0.01228 0.41369 11.3695
33 2IYA UDP 0.00002789 0.50628 11.7788
34 3E1T FAD 0.03156 0.40153 12.5
35 2ACV UDP 0.0003031 0.4485 13.4615
36 3OTH TYD 0.00001989 0.51882 20.3883
Pocket No.: 2; Query (leader) PDB : 1RRV; Ligand: TYD; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 1rrv.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZPD DPX 0.01713 0.40319 1.92308
2 3WGT FAD 0.02912 0.40942 2.88184
3 2VZZ SCA 0.0139 0.40749 3.21101
4 1QF9 C5P 0.02513 0.40202 4.80769
5 2NXW TPP 0.01729 0.40661 5.04808
6 1LYB IVA VAL VAL STA ALA STA 0.01415 0.40582 19.5876
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