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
25.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.27
Reason: no major geometry red flags detected
1 protein-contact clashes
45% of hydrophobic surface appears solvent-exposed (9/20 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 (-1.138 kcal/mol/HA)
✓ Good fit quality (FQ -10.61)
✓ Good H-bonds (4 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ High strain energy (25.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-30.718
kcal/mol
LE
-1.138
kcal/mol/HA
Fit Quality
-10.61
FQ (Leeson)
HAC
27
heavy atoms
MW
428
Da
LogP
4.48
cLogP
Final rank
4.5946
rank score
Inter norm
-1.113
normalised
Contacts
18
H-bonds 8
Interaction summary
HBA 4
HY 3
PI 0
CLASH 1
Interaction summary
HBA 4
HY 3
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 14 | Native recall | 0.67 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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 | ||
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
-30.718kcal/mol
Ligand efficiency (LE)
-1.1377kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.614
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
428.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.48
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
20.91kcal/mol
Minimised FF energy
-4.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
605.0Ų
Total solvent-accessible surface area of free ligand
BSA total
525.0Ų
Buried surface area upon binding
BSA apolar
382.2Ų
Hydrophobic contacts buried
BSA polar
142.8Ų
Polar contacts buried
Fraction buried
86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1335.8Ų
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
494.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)