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Receptor
PDB id Resolution Class Description Source Keywords
2NP9 2.45 Å EC: 1.13.11.- CRYSTAL STRUCTURE OF A DIOXYGENASE IN THE CROTONASE SUPERFAM STREPTOMYCES TOYOCAENSIS PROTEIN INHIBITOR COMPLEX OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR COFACTOR-INDEPENDENT DIOXYGENA VANCOMYCIN BIOSYNTHESIS. NATURE V. 447 342 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
OXY A:888;
B:888;
C:888;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
31.999 O2 O=O
YE1 A:999;
B:999;
C:999;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 2.7 uM
900.615 C29 H43 N8 O19 P3 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2NP9 2.45 Å EC: 1.13.11.- CRYSTAL STRUCTURE OF A DIOXYGENASE IN THE CROTONASE SUPERFAM STREPTOMYCES TOYOCAENSIS PROTEIN INHIBITOR COMPLEX OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR COFACTOR-INDEPENDENT DIOXYGENA VANCOMYCIN BIOSYNTHESIS. NATURE V. 447 342 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NP9 Ki = 2.7 uM YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
2 5KAG - YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NP9 Ki = 2.7 uM YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
2 5KAG - YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NP9 Ki = 2.7 uM YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
2 5KAG - YE1 C29 H43 N8 O19 P3 CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YE1; Similar ligands found: 144
No: Ligand ECFP6 Tc MDL keys Tc
1 YE1 1 1
2 SCO 0.8125 0.965517
3 0T1 0.809524 0.965517
4 COA 0.809524 0.965517
5 DCA 0.808 0.943182
6 30N 0.804688 0.884211
7 CMX 0.79845 0.965517
8 ETB 0.793651 0.910112
9 AMX 0.790698 0.976744
10 CAO 0.790698 0.933333
11 COS 0.790698 0.94382
12 ACO 0.778626 0.933333
13 FAM 0.778626 0.94382
14 FCX 0.778626 0.933333
15 BCA 0.773723 0.977273
16 HAX 0.772727 0.94382
17 3KK 0.766917 0.94382
18 FYN 0.766917 0.965517
19 SOP 0.761194 0.94382
20 COK 0.761194 0.94382
21 MCD 0.761194 0.94382
22 OXK 0.761194 0.94382
23 CA6 0.761194 0.857143
24 4CA 0.76087 0.977273
25 1VU 0.755556 0.933333
26 NMX 0.755556 0.893617
27 CO6 0.755556 0.94382
28 CMC 0.755556 0.94382
29 BYC 0.753623 0.965909
30 CAJ 0.75 0.94382
31 2MC 0.75 0.903226
32 SCD 0.75 0.965517
33 FAQ 0.748201 0.965909
34 3HC 0.744526 0.954545
35 IVC 0.744526 0.954545
36 A1S 0.744526 0.94382
37 MLC 0.744526 0.94382
38 1HE 0.744526 0.923077
39 BCO 0.744526 0.94382
40 3CP 0.741007 0.94382
41 COW 0.741007 0.955056
42 CAA 0.73913 0.954545
43 MCA 0.73913 0.933333
44 COO 0.73913 0.94382
45 SCA 0.733813 0.94382
46 2CP 0.733813 0.933333
47 MC4 0.733813 0.893617
48 S0N 0.732394 0.965909
49 2NE 0.732394 0.966292
50 IRC 0.728571 0.954545
51 CA8 0.728571 0.876289
52 COF 0.728571 0.923077
53 HGG 0.728571 0.94382
54 2KQ 0.728571 0.923077
55 1GZ 0.728571 0.933333
56 4CO 0.727273 0.977273
57 HXC 0.71831 0.923077
58 GRA 0.71831 0.94382
59 WCA 0.717241 0.966292
60 0FQ 0.715278 0.965909
61 TGC 0.713287 0.933333
62 CO8 0.708333 0.923077
63 1CZ 0.708333 0.933333
64 CIC 0.708333 0.94382
65 HFQ 0.707483 0.966292
66 MYA 0.703448 0.923077
67 5F9 0.703448 0.923077
68 DCC 0.703448 0.923077
69 UCC 0.703448 0.923077
70 MFK 0.703448 0.923077
71 ST9 0.703448 0.923077
72 4KX 0.70068 0.934066
73 0ET 0.69863 0.923077
74 01A 0.69863 0.923913
75 CS8 0.693878 0.913043
76 1CV 0.693878 0.94382
77 UOQ 0.689189 0.923077
78 NHW 0.689189 0.923077
79 HDC 0.689189 0.923077
80 NHM 0.689189 0.923077
81 MRS 0.684564 0.923077
82 MRR 0.684564 0.923077
83 F8G 0.681818 0.904255
84 DAK 0.68 0.934066
85 YNC 0.68 0.933333
86 1HA 0.679739 0.966292
87 8Z2 0.675497 0.913043
88 NHQ 0.666667 0.954545
89 COD 0.656716 0.954023
90 01K 0.653846 0.94382
91 COT 0.649682 0.965909
92 93P 0.648148 0.955056
93 CA3 0.641509 0.965909
94 CCQ 0.64 0.903226
95 7L1 0.633803 0.933333
96 CA5 0.631902 0.923913
97 93M 0.628743 0.955056
98 UCA 0.618182 0.944444
99 CO7 0.610738 0.94382
100 OXT 0.590909 0.904255
101 4BN 0.575419 0.904255
102 5TW 0.575419 0.904255
103 JBT 0.559783 0.885417
104 BSJ 0.553073 0.934066
105 PAP 0.544715 0.802326
106 HMG 0.5375 0.911111
107 COA PLM 0.530864 0.891304
108 PLM COA 0.530864 0.891304
109 ASP ASP ASP ILE CMC NH2 0.508571 0.901099
110 PPS 0.496124 0.726316
111 A3P 0.495935 0.790698
112 RFC 0.482353 0.944444
113 SFC 0.482353 0.944444
114 0WD 0.48 0.8
115 191 0.463415 0.838384
116 ACE SER ASP ALY THR NH2 COA 0.453125 0.901099
117 PTJ 0.439716 0.862069
118 3AM 0.435484 0.77907
119 PUA 0.427673 0.831461
120 A22 0.427536 0.825581
121 A2D 0.421875 0.813953
122 PAJ 0.421429 0.873563
123 3OD 0.41958 0.816092
124 AGS 0.41791 0.777778
125 SAP 0.41791 0.777778
126 ATR 0.41791 0.790698
127 HEJ 0.413534 0.813953
128 ATP 0.413534 0.813953
129 ADP 0.412214 0.813953
130 5FA 0.410448 0.813953
131 AQP 0.410448 0.813953
132 A2R 0.410072 0.804598
133 NJP 0.407643 0.83908
134 OAD 0.405594 0.816092
135 NA7 0.405594 0.848837
136 BA3 0.40458 0.813953
137 B4P 0.401515 0.813953
138 AP5 0.401515 0.813953
139 ANP 0.40146 0.795455
140 YAP 0.401361 0.83908
141 48N 0.401316 0.8
142 APR 0.4 0.793103
143 AR6 0.4 0.793103
144 2A5 0.4 0.837209
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: 87
This union binding pocket(no: 1) in the query (biounit: 2np9.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 1V6A TRE 1.50602
2 3X01 AMP 1.52672
3 5WXU FLC 1.59091
4 2G50 PYR 1.59091
5 1WOG 16D 1.96721
6 5U97 PIT 2.04545
7 5UI2 SUC 2.2082
8 3EW2 BTN 2.22222
9 4XH0 ADP 2.23325
10 3KLL MAL 2.27273
11 3HMO STU 2.33918
12 5YLF BGC 2.39521
13 2XZ9 PYR 2.46914
14 4CS9 AMP 2.6455
15 5OKT 9XK 2.86624
16 1RJW ETF 2.94985
17 2BMB PMM 2.95455
18 6E8I PTR 2.95858
19 3BP1 GUN 3.10345
20 2JAP J01 3.23887
21 5ZRR 9J3 3.39623
22 2BHZ MAL 3.40909
23 1TZD ADP 3.63636
24 1ZX5 LFR 3.66667
25 2Z49 AMG 3.7037
26 2Z48 A2G 3.7037
27 1P6O HPY 3.72671
28 5XH2 NPO 3.81679
29 2IF8 ADP 4.13223
30 4JGP PYR 4.14747
31 3FSY SCA 4.51807
32 4I9B 1KA 4.54545
33 3LJU IP9 4.66321
34 5UPK ANP 4.91329
35 4U36 TNR 5
36 1KZL CRM 5.28846
37 4URN NOV 5.33333
38 4OKD GLC GLC GLC 5.45455
39 1H8P PC 5.50459
40 5LV1 78T 6.07143
41 2ZL4 ALA ALA ALA ALA 6.12245
42 5WS9 OXL 6.13636
43 4B3J COA 6.25
44 5OCQ CIT 6.31579
45 4WGF HX2 6.34146
46 5LX9 OLB 6.69014
47 4Y4V DAL 6.78466
48 2NV2 GLN 6.86275
49 4ZNO SUC 7.16418
50 4IP7 FLC 7.5
51 1OYJ GSH 8.22511
52 5F90 GLA GAL 8.33333
53 1ON3 MCA 8.63636
54 5TVI O8N 8.69565
55 4ZDC CO8 9
56 3BY8 MLT 9.15493
57 5YRF GLC GLC 9.15493
58 5YRM BGC GLC 9.15493
59 5YRJ BGC GLC 9.15493
60 2FKA BEF 9.30233
61 4L8F MTX 9.9359
62 3O7J 2AL 10.0529
63 5J6Y BGC 10.1064
64 5J6Y GLC 10.1064
65 1KC7 PPR 10.2273
66 3BPX SAL 10.8108
67 2CBZ ATP 11.3924
68 1T0S BML 12.7907
69 1WDK N8E 12.9545
70 5X80 SAL 13.125
71 2FHE GSH 13.4259
72 2B1N LYS ALA SER VAL GLY 14.6341
73 5DUF G7A 14.8289
74 5FUS DAO 17.0732
75 5JBX COA 17.2414
76 5JBX MLI 17.2414
77 4QIJ 1HA 30.5389
78 1SG4 CO8 31.1538
79 4I4Z 2NE 32.7273
80 1JXZ BCA 33.0855
81 1NZY BCA 33.4572
82 4IZC 1GZ 33.8182
83 1DUB CAA 34.8659
84 2VSS ACO 36.5942
85 2VSU ACO 36.7273
86 4I42 1HA 37.5439
87 5ZAI COA 38.61
Pocket No.: 2; Query (leader) PDB : 2NP9; Ligand: YE1; 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: 2np9.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: 32
This union binding pocket(no: 3) in the query (biounit: 2np9.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 4LHM AZZ 1.59091
2 1ZGS XMM 1.59091
3 6GH9 MIX 1.64384
4 2Q8G AZX 1.9656
5 5KZV HCD 2.3622
6 2X1L MET 2.5
7 4L9I 8PR 2.95455
8 1KNM LAT 3.07692
9 5CX6 CDP 3.40909
10 2P3V SRT 3.51562
11 5T63 ALA ALA ALA ALA 3.54223
12 5DZT AMP 3.63636
13 6G33 5ID 3.83481
14 3L8G GMB 4.81283
15 6FLZ MMA 4.86111
16 5HVJ ANP 5.07937
17 2CIX CEJ 5.35117
18 5L8N 6RQ 5.46875
19 3TW1 AHN 5.48523
20 4IX4 ADP 5.68182
21 1VKF CIT 5.85106
22 4CIB 7UZ 5.90909
23 1CKM GTP 6.06061
24 3VV1 GAL FUC 6.25
25 5KXE 6Y2 6.58436
26 2Q89 6CS 6.61479
27 4OUC 5ID 9.52381
28 1Q8Y ADE 10.1877
29 2A19 ANP 11.9718
30 4PYA 2X3 13.6646
31 4BCQ TJF 17.608
32 2VSS V55 36.5942
Pocket No.: 4; Query (leader) PDB : 2NP9; Ligand: YE1; 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: 2np9.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: 17
This union binding pocket(no: 5) in the query (biounit: 2np9.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 2G2Y MLI 2.27273
2 5C9P FUC 3.63636
3 1POT SPD 3.69231
4 4ZVC BEZ 4.7619
5 4E28 9MZ 5.84615
6 4FFG LBS 5.90909
7 4JNJ BTN 6.08696
8 4LH7 1X8 6.50155
9 1FQK ALF 8.16327
10 5F90 LMR 8.33333
11 5W7B MYR 8.51064
12 5YRL GLC GLC 9.15493
13 5YRG BGC GLC 9.15493
14 4PTN PYR 9.62099
15 4PTN GXV 9.62099
16 6HDT BTN 9.77444
17 3IWD M2T 20.5882
Pocket No.: 6; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2np9.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2np9.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2np9.bio2) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2NP9; Ligand: YE1; Similar sites found with APoc: 1
This union binding pocket(no: 9) in the query (biounit: 2np9.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 2P7Q GG6 3.7594
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