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
37.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.95, Jaccard 0.91, H-bond role recall 0.45
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.245 kcal/mol/HA)
✓ Good fit quality (FQ -11.76)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Very high strain energy (37.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-34.867
kcal/mol
LE
-1.245
kcal/mol/HA
Fit Quality
-11.76
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
2.76
cLogP
Interaction summary
HB 11
HY 5
PI 1
CLASH 2
Interaction summary
HB 11
HY 5
PI 1
CLASH 2
| Final rank | 4.752 | Score | -34.867 |
|---|---|---|---|
| Inter norm | -1.260 | Intra norm | 0.015 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 11 |
| Artifact reason | geometry warning; 15 clashes; 3 protein clashes; high strain Δ 37.1 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.91 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 276 | 1.4370460415681932 | -0.857202 | -20.8428 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 1.5440426723862828 | -0.915782 | -15.5774 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 2.2845055573682136 | -0.837043 | -14.4333 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 328 | 3.9600681558418565 | -0.700868 | -19.9524 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 4.402454043048613 | -1.3024 | -32.5083 | 11 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 243 | 4.556144867088151 | -1.00584 | -21.4104 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 4.751862308706498 | -1.26026 | -34.8667 | 11 | 21 | 20 | 0.95 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-34.867kcal/mol
Ligand efficiency (LE)
-1.2452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.755
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.76
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-83.54kcal/mol
Minimised FF energy
-120.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
657.5Ų
Total solvent-accessible surface area of free ligand
BSA total
546.9Ų
Buried surface area upon binding
BSA apolar
415.2Ų
Hydrophobic contacts buried
BSA polar
131.7Ų
Polar contacts buried
Fraction buried
83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1372.5Ų
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
512.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)