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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
35.9 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.76, Jaccard 0.59, H-bond role recall 0.18
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
66% of hydrophobic surface is solvent-exposed (21/32 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 (-0.691 kcal/mol/HA)
✓ Good fit quality (FQ -7.07)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Very high strain energy (35.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-25.560
kcal/mol
LE
-0.691
kcal/mol/HA
Fit Quality
-7.07
FQ (Leeson)
HAC
37
heavy atoms
MW
505
Da
LogP
2.13
cLogP
Interaction summary
HB 9
HY 5
PI 1
CLASH 6
⚠ Exposure 65%
Interaction summary
HB 9
HY 5
PI 1
CLASH 6
⚠ Exposure 65%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
66% of hydrophobic surface is solvent-exposed (21/32 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 32
Buried (contacted) 11
Exposed 21
LogP 2.13
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 5.110 | Score | -25.560 |
|---|---|---|---|
| Inter norm | -0.813 | Intra norm | 0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 9 |
| Artifact reason | geometry warning; 18 clashes; 2 protein clashes; high strain Δ 35.9 | ||
| Residues |
ALA158
ALA24
ALA70
ASN126
ASN41
ASP68
GLN42
GLU73
GLY23
GLY25
GLY47
GLY71
LEU39
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.59 | RMSD | - |
| HB strict | 3 | Strict recall | 0.20 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 189 | 3.6139256947282776 | -0.596335 | -12.252 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 182 | 4.155325660406347 | -0.624276 | -21.2975 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 101 | 4.755589338185813 | -0.695614 | -22.0288 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 136 | 5.110190366967956 | -0.812608 | -25.56 | 9 | 22 | 16 | 0.76 | 0.18 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.560kcal/mol
Ligand efficiency (LE)
-0.6908kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.072
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
504.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
169.68kcal/mol
Minimised FF energy
133.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
794.2Ų
Total solvent-accessible surface area of free ligand
BSA total
653.1Ų
Buried surface area upon binding
BSA apolar
580.9Ų
Hydrophobic contacts buried
BSA polar
72.2Ų
Polar contacts buried
Fraction buried
82.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1601.3Ų
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
489.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)