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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
11.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.90, Jaccard 0.86, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (8/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.659 kcal/mol/HA)
✓ Good fit quality (FQ -14.15)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (11.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-34.828
kcal/mol
LE
-1.659
kcal/mol/HA
Fit Quality
-14.15
FQ (Leeson)
HAC
21
heavy atoms
MW
305
Da
LogP
0.95
cLogP
Interaction summary
HB 12
HY 9
PI 1
CLASH 1
⚠ Exposure 50%
Interaction summary
HB 12
HY 9
PI 1
CLASH 1
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (8/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 8
Exposed 8
LogP 0.95
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.265 | Score | -34.828 |
|---|---|---|---|
| Inter norm | -1.825 | Intra norm | 0.167 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU73
GLY23
GLY25
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.86 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 204 | 2.265390549677196 | -1.82522 | -34.828 | 12 | 20 | 19 | 0.90 | 0.36 | - | no | Current |
| 213 | 3.8266917662790605 | -1.28642 | -22.9226 | 4 | 18 | 1 | 0.05 | 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
-34.828kcal/mol
Ligand efficiency (LE)
-1.6585kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.146
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
305.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.95
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-63.06kcal/mol
Minimised FF energy
-74.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
573.5Ų
Total solvent-accessible surface area of free ligand
BSA total
519.6Ų
Buried surface area upon binding
BSA apolar
420.8Ų
Hydrophobic contacts buried
BSA polar
98.8Ų
Polar contacts buried
Fraction buried
90.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1344.0Ų
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
498.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)