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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.27
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.155 kcal/mol/HA)
✓ Good fit quality (FQ -10.50)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-28.867
kcal/mol
LE
-1.155
kcal/mol/HA
Fit Quality
-10.50
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
2.08
cLogP
Interaction summary
HB 10
HY 3
PI 0
CLASH 3
⚠ Exposure 66%
Interaction summary
HB 10
HY 3
PI 0
CLASH 3
⚠ Exposure 66%
Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18
Buried (contacted) 6
Exposed 12
LogP 2.08
H-bonds 10
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (3/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.727 | Score | -28.867 |
|---|---|---|---|
| Inter norm | -1.238 | Intra norm | 0.083 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 4 protein clashes | ||
| Residues |
ALA24
ALA40
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
ILE46
LEU31
LEU39
LYS26
PHE38
SER22
SER27
SER28
THR44
| ||
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 12 | Native recall | 0.57 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 4 | HB residue recall | 0.36 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.867kcal/mol
Ligand efficiency (LE)
-1.1547kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.497
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
344.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.08
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.41kcal/mol
Minimised FF energy
47.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
544.4Ų
Total solvent-accessible surface area of free ligand
BSA total
475.7Ų
Buried surface area upon binding
BSA apolar
329.3Ų
Hydrophobic contacts buried
BSA polar
146.4Ų
Polar contacts buried
Fraction buried
87.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1264.2Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
493.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)