Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
18.9 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.634 kcal/mol/HA)
✓ Good fit quality (FQ -6.18)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-19.663
kcal/mol
LE
-0.634
kcal/mol/HA
Fit Quality
-6.18
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Interaction summary
HB 2
HY 23
PI 3
CLASH 3
Interaction summary
HB 2
HY 23
PI 3
CLASH 3
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 0.271 | Score | -19.663 |
|---|---|---|---|
| Inter norm | -0.811 | Intra norm | 0.177 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 2 |
| Artifact reason | geometry warning; 8 clashes; 1 protein contact clash; 2 severe cofactor-context clashes | ||
| Residues |
ARG17
ASP232
GLY225
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR191
TYR194
VAL230
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 458 | 0.27097943228209714 | -0.811185 | -19.6635 | 2 | 14 | 13 | 0.68 | 0.20 | - | no | Current |
| 513 | 0.9544730494110983 | -0.848599 | -22.718 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 139 | 1.2196504051403532 | -0.732121 | -21.3242 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 506 | 1.3741049807450607 | -0.848148 | -20.44 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 114 | 1.8007768117229013 | -0.767307 | -20.1444 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 131 | 1.8058017168282356 | -0.940039 | -24.6674 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 117 | 2.0182178879377184 | -0.829303 | -24.0955 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 485 | 2.0994881049338083 | -0.856427 | -22.7639 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 105 | 2.2832214801183897 | -0.874039 | -22.0808 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 453 | 2.83121549954444 | -0.908661 | -22.7336 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 2.8591163001678837 | -0.882026 | -22.5359 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 2.939096492500812 | -0.773608 | -21.4384 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 2.9866007130431282 | -0.949521 | -25.285 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 3.435617077931159 | -1.00835 | -28.0542 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 3.5725886357035477 | -0.950541 | -26.1853 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 89 | 3.588860201862459 | -0.897555 | -24.8412 | 10 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 4.484716716621432 | -0.989791 | -28.8598 | 6 | 13 | 12 | 0.63 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.663kcal/mol
Ligand efficiency (LE)
-0.6343kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.180
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
26.37kcal/mol
Minimised FF energy
7.50kcal/mol
SASA & burial
✓ computed
SASA (unbound)
693.4Ų
Total solvent-accessible surface area of free ligand
BSA total
533.5Ų
Buried surface area upon binding
BSA apolar
329.7Ų
Hydrophobic contacts buried
BSA polar
203.8Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1621.3Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1027.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)