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 medium
Native strong
SASA done
Strain ΔE
33.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.27
Reason: no major geometry red flags detected
1 protein-contact clashes
94% of hydrophobic surface is solvent-exposed (17/18 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.016 kcal/mol/HA)
✓ Good fit quality (FQ -9.48)
✓ Good H-bonds (4 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (33.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.438
kcal/mol
LE
-1.016
kcal/mol/HA
Fit Quality
-9.48
FQ (Leeson)
HAC
27
heavy atoms
MW
408
Da
LogP
2.56
cLogP
Final rank
3.6973
rank score
Inter norm
-1.169
normalised
Contacts
22
H-bonds 8
Interaction summary
HBA 4
HY 2
PI 0
CLASH 1
Interaction summary
HBA 4
HY 2
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.65 | 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | 3.285700678836707 | -0.723755 | -10.8095 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 3.6972539831852793 | -1.16852 | -27.4379 | 8 | 22 | 17 | 0.81 | 0.27 | - | no | Current |
| 390 | 4.168243620208268 | -0.929845 | -20.354 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 4.504355784231469 | -1.05457 | -17.1995 | 12 | 18 | 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
-27.438kcal/mol
Ligand efficiency (LE)
-1.0162kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.481
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.56
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
27.58kcal/mol
Minimised FF energy
-5.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
653.7Ų
Total solvent-accessible surface area of free ligand
BSA total
580.8Ų
Buried surface area upon binding
BSA apolar
435.4Ų
Hydrophobic contacts buried
BSA polar
145.4Ų
Polar contacts buried
Fraction buried
88.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1377.9Ų
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
492.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)