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 medium
Native strong
SASA done
Strain ΔE
14.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.82, H-bond role recall 0.55
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular 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 (-1.307 kcal/mol/HA)
✓ Good fit quality (FQ -11.35)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (14.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-28.752
kcal/mol
LE
-1.307
kcal/mol/HA
Fit Quality
-11.35
FQ (Leeson)
HAC
22
heavy atoms
MW
297
Da
LogP
2.30
cLogP
Interaction summary
HB 8
HY 8
PI 1
CLASH 3
⚠ Exposure 50%
Interaction summary
HB 8
HY 8
PI 1
CLASH 3
⚠ Exposure 50%
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
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 2.3
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.145 | Score | -28.752 |
|---|---|---|---|
| Inter norm | -1.429 | Intra norm | 0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU73
GLY23
GLY25
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
THR44
| ||
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 220 | 0.3651391185133525 | -1.45139 | -23.7405 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 192 | 0.4571207130802301 | -1.18119 | -19.2496 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 237 | 1.5063260990891212 | -1.13516 | -23.1709 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 1.5181578036895516 | -1.089 | -19.0581 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 243 | 1.7178078774494703 | -1.28667 | -20.7882 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 232 | 1.8651070569406785 | -1.47707 | -29.7815 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 198 | 2.1445626433417684 | -1.42852 | -28.7517 | 8 | 19 | 18 | 0.86 | 0.55 | - | no | Current |
| 213 | 2.3624501248232654 | -1.20095 | -22.4306 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 155 | 2.5177967963534 | -1.60533 | -28.0634 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 2.61548570124989 | -0.940053 | -20.2644 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 2.843997714984992 | -1.28647 | -22.6883 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 153 | 3.038012358487256 | -1.13257 | -24.4214 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 223 | 4.2149665993990615 | -1.33738 | -26.7053 | 8 | 11 | 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
-28.752kcal/mol
Ligand efficiency (LE)
-1.3069kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.346
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
297.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.30
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.16kcal/mol
Minimised FF energy
28.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
529.4Ų
Total solvent-accessible surface area of free ligand
BSA total
473.9Ų
Buried surface area upon binding
BSA apolar
352.7Ų
Hydrophobic contacts buried
BSA polar
121.1Ų
Polar contacts buried
Fraction buried
89.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1264.8Ų
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
494.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)