Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
20.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.68, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
36% of hydrophobic surface appears solvent-exposed (10/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.643 kcal/mol/HA)
✓ Good fit quality (FQ -6.67)
✓ Good H-bonds (3 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (20.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (13)
Score
-25.075
kcal/mol
LE
-0.643
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
39
heavy atoms
MW
563
Da
LogP
5.00
cLogP
Interaction summary
HB 3
HY 24
PI 3
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 3
HY 24
PI 3
CLASH 2
⚠ Exposure 35%
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
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (10/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 18
Exposed 10
LogP 5.0
H-bonds 3
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.280 | Score | -25.075 |
|---|---|---|---|
| Inter norm | -0.617 | Intra norm | -0.026 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 2 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 20.9 | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
ARG287
| ||
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 | 0.68 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 475 | 1.280287287729594 | -0.617165 | -25.0747 | 3 | 13 | 13 | 0.68 | 0.20 | - | no | Current |
| 463 | 2.6296067961054295 | -0.682535 | -26.5323 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 514 | 3.7948270720513495 | -0.709367 | -28.2621 | 7 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 4.655184917891928 | -0.82917 | -34.339 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 457 | 5.557439725654371 | -0.634517 | -20.1581 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 460 | 5.792579168189608 | -0.711207 | -22.3926 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.075kcal/mol
Ligand efficiency (LE)
-0.6429kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.672
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
563.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.12kcal/mol
Minimised FF energy
92.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
864.2Ų
Total solvent-accessible surface area of free ligand
BSA total
504.9Ų
Buried surface area upon binding
BSA apolar
418.7Ų
Hydrophobic contacts buried
BSA polar
86.1Ų
Polar contacts buried
Fraction buried
58.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1841.1Ų
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
1093.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)