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
20.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.54, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
52% of hydrophobic surface appears solvent-exposed (13/25 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 (-1.080 kcal/mol/HA)
✓ Good fit quality (FQ -10.52)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (20.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-33.471
kcal/mol
LE
-1.080
kcal/mol/HA
Fit Quality
-10.52
FQ (Leeson)
HAC
31
heavy atoms
MW
416
Da
LogP
3.75
cLogP
Interaction summary
HB 10
HY 5
PI 1
CLASH 1
⚠ Exposure 52%
Interaction summary
HB 10
HY 5
PI 1
CLASH 1
⚠ Exposure 52%
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
Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (13/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 12
Exposed 13
LogP 3.75
H-bonds 10
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.647 | Score | -33.471 |
|---|---|---|---|
| Inter norm | -1.082 | Intra norm | 0.002 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 10 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes; moderate strain Δ 20.5 | ||
| Residues |
ALA24
ALA40
ALA70
ASN41
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 242 | 1.933586563779863 | -0.937196 | -21.0402 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 211 | 4.646651250388195 | -1.08199 | -33.4713 | 10 | 22 | 15 | 0.71 | 0.36 | - | no | Current |
| 278 | 4.71083283317276 | -0.683344 | -18.5845 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 219 | 5.35149050242467 | -0.857702 | -23.3039 | 4 | 12 | 0 | 0.00 | 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
-33.471kcal/mol
Ligand efficiency (LE)
-1.0797kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.519
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.75
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
69.25kcal/mol
Minimised FF energy
48.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
713.5Ų
Total solvent-accessible surface area of free ligand
BSA total
630.1Ų
Buried surface area upon binding
BSA apolar
560.6Ų
Hydrophobic contacts buried
BSA polar
69.5Ų
Polar contacts buried
Fraction buried
88.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1496.0Ų
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
515.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)