Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
35.0 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.95, Jaccard 0.74, H-bond role recall 0.18
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (11/28 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 (-0.785 kcal/mol/HA)
✓ Good fit quality (FQ -7.98)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Very high strain energy (35.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-28.264
kcal/mol
LE
-0.785
kcal/mol/HA
Fit Quality
-7.98
FQ (Leeson)
HAC
36
heavy atoms
MW
482
Da
LogP
4.49
cLogP
Interaction summary
HB 7
HY 12
PI 1
CLASH 8
⚠ Exposure 39%
Interaction summary
HB 7
HY 12
PI 1
CLASH 8
⚠ Exposure 39%
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (11/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 17
Exposed 11
LogP 4.49
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 5.980 | Score | -28.264 |
|---|---|---|---|
| Inter norm | -0.852 | Intra norm | 0.066 |
| Top1000 | no | Excluded | no |
| Contacts | 26 | H-bonds | 7 |
| Artifact reason | geometry warning; 17 clashes; 3 protein clashes; high strain Δ 35.0 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 2 | Strict recall | 0.13 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| HB same residue | 2 | HB residue recall | 0.18 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 604 | 2.391433960054099 | -0.72906 | -17.4267 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 3.1727607344736213 | -0.598552 | -19.2757 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 3.398860628331752 | -0.818739 | -26.296 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 4.123937815695857 | -0.730944 | -28.0767 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 608 | 4.229730232478214 | -0.787302 | -33.8349 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 5.9796918661171885 | -0.85151 | -28.2644 | 7 | 26 | 20 | 0.95 | 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
-28.264kcal/mol
Ligand efficiency (LE)
-0.7851kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.980
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
481.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.49
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
152.47kcal/mol
Minimised FF energy
117.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
766.9Ų
Total solvent-accessible surface area of free ligand
BSA total
664.4Ų
Buried surface area upon binding
BSA apolar
550.0Ų
Hydrophobic contacts buried
BSA polar
114.4Ų
Polar contacts buried
Fraction buried
86.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1487.9Ų
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
498.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)