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
12.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.58, H-bond role recall 0.27
Reason: no major geometry red flags detected
2 protein-contact clashes
82% of hydrophobic surface is solvent-exposed (27/33 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 (-0.864 kcal/mol/HA)
✓ Good fit quality (FQ -8.78)
✓ Good H-bonds (4 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Moderate strain (12.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (18)
Score
-31.098
kcal/mol
LE
-0.864
kcal/mol/HA
Fit Quality
-8.78
FQ (Leeson)
HAC
36
heavy atoms
MW
465
Da
LogP
8.45
cLogP
Interaction summary
HB 4
HY 1
PI 1
CLASH 2
⚠ Exposure 81%
Interaction summary
HB 4
HY 1
PI 1
CLASH 2
⚠ Exposure 81%
Solvent-exposed hydrophobic surface — desolvation penalty likely
82% of hydrophobic surface is solvent-exposed (27/33 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 33
Buried (contacted) 6
Exposed 27
LogP 8.45
H-bonds 4
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 1.716 | Score | -31.098 |
|---|---|---|---|
| Inter norm | -0.891 | Intra norm | 0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | geometry warning; 18 clashes; 4 protein contact clashes | ||
| Residues |
ALA158
ASN126
ASN41
ASP129
ASP68
GLU73
GLY23
GLY25
GLY71
LEU130
LYS127
LYS128
LYS159
LYS26
PHE38
SER157
SER27
SER28
THR44
THR69
| ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 3 | Strict recall | 0.20 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.098kcal/mol
Ligand efficiency (LE)
-0.8638kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.780
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
464.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
8.45
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.25kcal/mol
Minimised FF energy
84.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
803.7Ų
Total solvent-accessible surface area of free ligand
BSA total
600.7Ų
Buried surface area upon binding
BSA apolar
559.7Ų
Hydrophobic contacts buried
BSA polar
40.9Ų
Polar contacts buried
Fraction buried
74.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1572.2Ų
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
557.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)