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Receptor
PDB id Resolution Class Description Source Keywords
2CWH 1.7 Å EC: 1.5.1.- CRYSTAL STRUCTURE OF DELTA1-PIPERIDEINE-2-CARBOXYLATE REDUCTASE FROM PSEUDOMONAS SYRINGAE COMPLEXED WITH NADPH A ND PYRROLE-2-CARBOXYLATE PSEUDOMONAS SYRINGAE PV. TOMATO NADPH DEPENDENT ENZYME OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF DELTA1-PIPERIDEINE-2-CARBOXYLATE/DELTA1-PYRROLINE-2-CARBOXYLATE REDUCTASE BELONGING TO A NEW FAMILY OF NAD(P)H-DEPENDENT OXIDOREDUCTASES: CONFORMATIONAL CHANGE, SUBSTRATE RECOGNITION, AND STEREOCHEMISTRY OF THE REACTION J.BIOL.C
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:2510;
B:1510;
Valid;
Valid;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
PYC A:2520;
B:1520;
Valid;
Valid;
none;
none;
submit data
110.091 C5 H4 N O2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CWH 1.7 Å EC: 1.5.1.- CRYSTAL STRUCTURE OF DELTA1-PIPERIDEINE-2-CARBOXYLATE REDUCTASE FROM PSEUDOMONAS SYRINGAE COMPLEXED WITH NADPH A ND PYRROLE-2-CARBOXYLATE PSEUDOMONAS SYRINGAE PV. TOMATO NADPH DEPENDENT ENZYME OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF DELTA1-PIPERIDEINE-2-CARBOXYLATE/DELTA1-PYRROLINE-2-CARBOXYLATE REDUCTASE BELONGING TO A NEW FAMILY OF NAD(P)H-DEPENDENT OXIDOREDUCTASES: CONFORMATIONAL CHANGE, SUBSTRATE RECOGNITION, AND STEREOCHEMISTRY OF THE REACTION J.BIOL.C
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CWH - PYC C5 H4 N O2 c1cc([nH]c....
2 2CWF - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CWH - PYC C5 H4 N O2 c1cc([nH]c....
2 2CWF - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CWH - PYC C5 H4 N O2 c1cc([nH]c....
2 2CWF - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Ligand no: 2; Ligand: PYC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 PYC 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CWH; Ligand: NDP; Similar sites found with APoc: 120
This union binding pocket(no: 1) in the query (biounit: 2cwh.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 4CQK PIO None
2 5KK4 44E None
3 5OCQ CIT 1.05263
4 2B56 U5P 1.45773
5 4NZ6 DGL 1.91693
6 3SHR CMP 2.00669
7 1Q19 SSC 2.04082
8 3G5N PB2 2.04082
9 1GOJ ADP 2.04082
10 2QS8 MET 2.04082
11 2VVG ADP 2.33236
12 3H4L ANP 2.33236
13 4OKE AMP 2.38095
14 4GO7 THR 2.5
15 5EQ8 HSO 2.52708
16 5NC1 NAG 2.53165
17 1GPM AMP 2.62391
18 2CXG GLC GLC 2.62391
19 2BOI MFU 2.65487
20 3L8G GMB 2.6738
21 2G30 ALA ALA PHE 2.71318
22 6A46 DCM 2.73438
23 3BY8 MLT 2.8169
24 3TY5 ATP 2.91545
25 3TDV GDP 2.94118
26 1SBR VIB 3
27 5FUI APY 3.0303
28 4FK7 P34 3.05677
29 5JBX MLI 3.06513
30 3BJE URA 3.207
31 3OF1 CMP 3.25203
32 3N9R TD3 3.25733
33 4U00 ADP 3.27869
34 1RRC ADP 3.32226
35 1O9W NAG 3.38983
36 3UEC ALA ARG TPO LYS 3.42466
37 2Z3U CRR 3.49854
38 2AWN ADP 3.49854
39 5ZYN SIN 3.49854
40 2GKS ADP 3.49854
41 1RDL MMA 3.53982
42 2YIP YIO 3.62319
43 3S6X SIA GAL BGC 3.69231
44 2VWT PYR 3.74532
45 5NM7 GLY 3.7594
46 5LFV SIA GAL NAG 3.78549
47 5W75 SUC 3.79009
48 2WDQ TEO 3.79009
49 5FJJ MAN 3.79009
50 5FPE 3TR 3.79009
51 5WXU FLC 3.79009
52 3LRE ADP 3.79009
53 5GVR LMR 3.84615
54 5YLF BGC 4.19162
55 5C8W PCG 4.1958
56 3SJK LYS PRO VAL LEU ARG THR ALA 4.21053
57 1WLJ U5P 4.2328
58 5AOG IAC 4.23453
59 1KSK URA 4.2735
60 1PVC ILE SER GLU VAL 4.42804
61 3AB4 THR 4.49438
62 3WG3 A2G GAL NAG FUC 4.49438
63 2DTJ THR 4.49438
64 1B0U ATP 4.58015
65 3N2O AG2 4.66472
66 4FOU C2E 4.92424
67 4TVD BGC 4.95627
68 2X1L MET 4.95627
69 3OCP CMP 5.03597
70 1G6H ADP 5.05837
71 5L3S G 5.06757
72 1PNF NDG NAG 5.09554
73 1U0J ADP 5.24345
74 1RL4 BRR 5.24781
75 4CS9 AMP 5.29101
76 5A04 BGC 5.30973
77 3BP1 GUN 5.51724
78 4Y4V DAL 5.60472
79 6FU4 HSM 5.7971
80 3RC3 ANP 5.8309
81 5H4S RAM 5.98592
82 4FGC PQ0 6.06061
83 3A4M ADP 6.15385
84 4CCK OGA 6.41399
85 1VBO MAN MAN MAN 6.41399
86 5E5U MLI 6.53266
87 1XPJ TLA 7.14286
88 1RZM E4P 7.39645
89 2IDO TMP 7.52688
90 5H9P TD2 7.59494
91 5A96 GTP 7.63052
92 3FW3 GLC 7.89474
93 2GAG FOA 8.08081
94 4G86 BNT 8.4507
95 1FUR MLT 8.74636
96 4JH6 FCN 9.42029
97 5AHO TLA 9.52381
98 2H88 TEO 10.7143
99 1GXU 2HP 10.989
100 3PNA CMP 11.039
101 2J5V PCA 11.0787
102 3LN9 FLC 11.5108
103 1QKQ MAN 11.9718
104 3NOJ PYR 12.605
105 2GN2 C5P 13.1579
106 5URY PAM 14.3836
107 4WVW SLT 15.2778
108 4YMU ATP 16.8182
109 2BOS GLA GAL GLC NBU 22.0588
110 2BOS GLA GAL 22.0588
111 2BOS GLA GAL GLC 22.0588
112 2DT9 THR 26.3473
113 4CCN OGA 28.5714
114 1Z2I NAD 38.1924
115 1S20 NAD 42.3529
116 2X06 NAD 42.8571
117 4FJU NAI 44.3149
118 4FJU GLV 44.3149
119 1VBI NAD 45.7726
120 1V9N NDP 47.2303
Pocket No.: 2; Query (leader) PDB : 2CWH; Ligand: NDP; Similar sites found with APoc: 16
This union binding pocket(no: 2) in the query (biounit: 2cwh.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2JDU MFU None
2 2Z9I GLY ALA THR VAL 1.85185
3 4B5W PYR 1.95312
4 3GD8 GOL 2.24215
5 3B6O TMP 2.42915
6 4LIT AKG 2.91545
7 5KIQ SIA GAL NAG FUC 4.06091
8 5T96 79J 4.38596
9 3ITJ CIT 5.32544
10 2OFD NGA 7.04225
11 1JOC ITP 9.6
12 5H9O GLC 10.2273
13 2BMR 3NT 11.8557
14 2YBP 2HG 13.9942
15 2OS2 OGA 13.9942
16 2P5B OGA 18.1818
Pocket No.: 3; Query (leader) PDB : 2CWH; Ligand: PYC; Similar sites found with APoc: 120
This union binding pocket(no: 3) in the query (biounit: 2cwh.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 4CQK PIO None
2 5KK4 44E None
3 1MJT ITU 0.874636
4 5OCQ CIT 1.05263
5 2B56 U5P 1.45773
6 2Z9I GLY ALA THR VAL 1.85185
7 4NZ6 DGL 1.91693
8 3SHR CMP 2.00669
9 1Q19 SSC 2.04082
10 3G5N PB2 2.04082
11 2QS8 MET 2.04082
12 2VVG ADP 2.33236
13 3H4L ANP 2.33236
14 4OKE AMP 2.38095
15 4GO7 THR 2.5
16 5EQ8 HSO 2.52708
17 5NC1 NAG 2.53165
18 4XDA RIB 2.589
19 1GPM AMP 2.62391
20 2CXG GLC GLC 2.62391
21 4XGU ADP 2.62391
22 1EI6 PPF 2.62391
23 5O9W AKG 2.62391
24 3L8G GMB 2.6738
25 2G30 ALA ALA PHE 2.71318
26 4FK7 P34 3.05677
27 5JBX MLI 3.06513
28 3X01 AMP 3.207
29 3BJE URA 3.207
30 2UYQ SAM 3.22581
31 3OF1 CMP 3.25203
32 4U00 ADP 3.27869
33 1RRC ADP 3.32226
34 3UEC ALA ARG TPO LYS 3.42466
35 2Z3U CRR 3.49854
36 2AWN ADP 3.49854
37 5ZYN SIN 3.49854
38 4XDY HIO 3.5503
39 4X1Z FUC GAL NDG 3.61446
40 2YIP YIO 3.62319
41 3S6X SIA GAL BGC 3.69231
42 2ZL7 FUC GAL NGA 3.72881
43 2VWT PYR 3.74532
44 5TV6 PML 3.75
45 4D3S BOG 3.75427
46 5NM7 GLY 3.7594
47 5LFV SIA GAL NAG 3.78549
48 5W75 SUC 3.79009
49 2WDQ TEO 3.79009
50 5FJJ MAN 3.79009
51 3LRE ADP 3.79009
52 2G50 PYR 3.79009
53 5GVR LMR 3.84615
54 5KIQ SIA GAL NAG FUC 4.06091
55 5YLF BGC 4.19162
56 5C8W PCG 4.1958
57 3SJK LYS PRO VAL LEU ARG THR ALA 4.21053
58 1KSK URA 4.2735
59 4K6B GLU 4.34783
60 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 4.37318
61 5T96 79J 4.38596
62 1PVC ILE SER GLU VAL 4.42804
63 3AB4 THR 4.49438
64 3WG3 A2G GAL NAG FUC 4.49438
65 2DTJ THR 4.49438
66 3ZXE PGZ 4.51128
67 1B0U ATP 4.58015
68 5W1E PHB 4.94297
69 2X1L MET 4.95627
70 3OCP CMP 5.03597
71 1G6H ADP 5.05837
72 5L3S G 5.06757
73 1PNF NDG NAG 5.09554
74 1U0J ADP 5.24345
75 1RL4 BRR 5.24781
76 4CS9 AMP 5.29101
77 4L4J NAG NAG BMA MAN NAG 5.42986
78 3BP1 GUN 5.51724
79 4Y4V DAL 5.60472
80 3RC3 ANP 5.8309
81 5MTE BB2 5.83942
82 4FGC PQ0 6.06061
83 3A4M ADP 6.15385
84 4CCK OGA 6.41399
85 5E5U MLI 6.53266
86 1NKI PPF 6.66667
87 1MFI FHC 7.01754
88 1XPJ TLA 7.14286
89 1RZM E4P 7.39645
90 1N1V DAN 7.58017
91 5H9P TD2 7.59494
92 5A96 GTP 7.63052
93 3FW3 GLC 7.89474
94 2GAG FOA 8.08081
95 4CUB GAL NAG 8.19672
96 1FUR MLT 8.74636
97 4WBD CIT 9.32945
98 5AHO TLA 9.52381
99 2H88 TEO 10.7143
100 1GXU 2HP 10.989
101 3PNA CMP 11.039
102 2J5V PCA 11.0787
103 3LN9 FLC 11.5108
104 3ZVS MLI 11.875
105 3NOJ PYR 12.605
106 5URY PAM 14.3836
107 4YMU ATP 16.8182
108 5FH7 5XL 18.5484
109 2BOS GLA GAL GLC NBU 22.0588
110 2BOS GLA GAL 22.0588
111 2BOS GLA GAL GLC 22.0588
112 2DT9 THR 26.3473
113 6C0B PAM 26.9231
114 1Z2I NAD 38.1924
115 1S20 NAD 42.3529
116 2X06 NAD 42.8571
117 4FJU GLV 44.3149
118 4FJU NAI 44.3149
119 1VBI NAD 45.7726
120 1V9N NDP 47.2303
Pocket No.: 4; Query (leader) PDB : 2CWH; Ligand: PYC; Similar sites found with APoc: 22
This union binding pocket(no: 4) in the query (biounit: 2cwh.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 1LNX URI None
2 4B5W PYR 1.95312
3 3GD8 GOL 2.24215
4 2H6B 3C4 2.4
5 3B6O TMP 2.42915
6 5EVY SAL 2.62391
7 6A46 DCM 2.73438
8 3TY5 ATP 2.91545
9 1SBR VIB 3
10 3N9R TD3 3.25733
11 1O9W NAG 3.38983
12 5WXU FLC 3.79009
13 5KXQ GDP 4.37318
14 3FJG 3PG 4.78088
15 1WD4 AHR 6.12245
16 3UWB BB2 8.44156
17 3KDM TES 9.33333
18 4K7O EKZ 9.52381
19 1JOC ITP 9.6
20 1QKQ MAN 11.9718
21 5C79 PBU 12.6667
22 5KY4 GDP 20
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